Picard file error

[Shivani-kushwaha]

Hello,
I'm running into the following error whenever I'm trying to run the pipeline on MAcOS, any help is appreciated!
==================================== Bulk data analysis pipeline will run ==============================================================

Input FASTQ folder: /Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/exampleData

Sample name: GATA1_D7_30min_chr11

Workdir folder: /Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11

Experiment name: GATA1_D7_30min_chr11

Experiment type: CUT&RUN

Reference genome: hg38

Spike-in genome: FALSE

Spike-in normalization: FALSE

Fragment 120 filtration: TRUE

=================================================================================================================================
[info] Input file is GATA1_D7_30min_chr11_R1_001.fastq.gz and GATA1_D7_30min_chr11_R2_001.fastq.gz
Sun Jan 7 16:46:07 EST 2024
[info] Trimming file GATA1_D7_30min_chr11 ...
Sun Jan 7 16:46:07 EST 2024
[info] Use Truseq adaptor as default
[info] Second stage trimming GATA1_D7_30min_chr11 ...
Sun Jan 7 16:46:14 EST 2024
[info] Aligning file GATA1_D7_30min_chr11 to reference genome...
Sun Jan 7 16:46:24 EST 2024
[info] Bowtie2 command: --dovetail --phred33
[info] The dovetail mode is enabled [as parameter frag_120 is on]
[info] FASTQ files won't be aligned to the spike-in genome
[info] Filtering unmapped fragments... GATA1_D7_30min_chr11.bam
Sun Jan 7 16:46:24 EST 2024
[info] Sorting BAM... GATA1_D7_30min_chr11.bam
Sun Jan 7 16:46:24 EST 2024
INFO 2024-01-07 16:46:24 SortSam

********** NOTE: Picard's command line syntax is changing.

---

********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)

---

********** The command line looks like this in the new syntax:

---

********** SortSam -INPUT sorted/GATA1_D7_30min_chr11.step1.bam -OUTPUT sorted/GATA1_D7_30min_chr11.bam -SORT_ORDER coordinate -VALIDATION_STRINGENCY SILENT -TMP_DIR /Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/logs

---

16:46:24.792 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/install/picard-2.8.0.jar!/com/intel/gkl/native/libgkl_compression.dylib
16:46:24.814 WARN NativeLibraryLoader - Unable to load libgkl_compression.dylib from native/libgkl_compression.dylib (Can't load library: /Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/logs/libgkl_compression3199524088769265004.dylib)
16:46:24.814 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/install/picard-2.8.0.jar!/com/intel/gkl/native/libgkl_compression.dylib
16:46:24.819 WARN NativeLibraryLoader - Unable to load libgkl_compression.dylib from native/libgkl_compression.dylib (Can't load library: /Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/logs/libgkl_compression8273045536062371726.dylib)
[Sun Jan 07 16:46:24 EST 2024] SortSam INPUT=sorted/GATA1_D7_30min_chr11.step1.bam OUTPUT=sorted/GATA1_D7_30min_chr11.bam SORT_ORDER=coordinate TMP_DIR=[/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/logs] VALIDATION_STRINGENCY=SILENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Sun Jan 07 16:46:24 EST 2024] Executing as [email protected] on Mac OS X 14.1.2 aarch64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_391-b13; Deflater: Jdk; Inflater: Jdk; Provider GCS is not available; Picard version: 2.21.7-SNAPSHOT
16:46:24.837 WARN IntelDeflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
16:46:24.849 WARN IntelDeflaterFactory - IntelDeflater is not supported, using Java.util.zip.Deflater
INFO 2024-01-07 16:46:24 SortSam Finished reading inputs, merging and writing to output now.
[Sun Jan 07 16:46:24 EST 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=257425408
[info] Marking duplicates... GATA1_D7_30min_chr11.bam
Sun Jan 7 16:46:24 EST 2024
[info] Removing duplicates... GATA1_D7_30min_chr11.bam
Sun Jan 7 16:46:25 EST 2024
[info] Filtering to <120bp... dup.marked and dedup BAMs
Sun Jan 7 16:46:25 EST 2024
[info] Creating bam index files... GATA1_D7_30min_chr11.bam
Sun Jan 7 16:46:25 EST 2024
[info] Reads shifting
Sun Jan 7 16:46:25 EST 2024
[info] Your data won't be shifted as the experiment_type is specified as CUT&RUN...
[info] Peak calling using MACS2... GATA1_D7_30min_chr11.bam
[info] Logs are stored in /Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/logs
Sun Jan 7 16:46:25 EST 2024
[info] Peak calling with BAM file with NO duplications
[info] macs2 narrow peak calling
[info] macs2 broad peak calling
[info] Getting broad peak summits
Traceback (most recent call last):
File "/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/install/get_summits_broadPeak.py", line 14, in
f = open(sys.argv[1])
FileNotFoundError: [Errno 2] No such file or directory: '/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/peakcalling/macs2.broad/GATA1_D7_30min_chr11_peaks.broadPeak'
[info] SEACR stringent peak calling
Traceback (most recent call last):
File "/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/install/change.bdg.py", line 12, in
f = open(sys.argv[1])
FileNotFoundError: [Errno 2] No such file or directory: '/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/peakcalling/seacr/GATA1_D7_30min_chr11_treat_pileup.bdg'
Calling enriched regions without control file
Proceeding without normalization of control to experimental bedgraph
Using stringent threshold
Creating experimental AUC file: Sun Jan 7 16:46:26 EST 2024
/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/install/SEACR_1.1.sh: line 103: 0I?e1?z۳0???.auc.bed: Illegal byte sequence
Unable to access /Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/peakcalling/seacr/GATA1_D7_30min_chr11_treat.stringent.bed
Traceback (most recent call last):
File "/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/install/get_summits_seacr.py", line 14, in
f = open(sys.argv[1])
FileNotFoundError: [Errno 2] No such file or directory: '/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/peakcalling/seacr/GATA1_D7_30min_chr11_treat.stringent.bed'
[info] Generating the normalized signal file with BigWig format...
Sun Jan 7 16:46:26 EST 2024
cp: /Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/peakcalling/macs2.narrow/GATA1_D7_30min_chr11.cpm.norm.bw: No such file or directory
cp: /Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/peakcalling/macs2.narrow/GATA1_D7_30min_chr11.cpm.norm.bw: No such file or directory
[info] Your bigwig file won't be normalized with spike-in reads
[info] Input file is /Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/bulk-example-test/GATA1_D7_30min_chr11/peakcalling/macs2.narrow/GATA1_D7_30min_chr11_peaks.narrowPeak
cat: GATA1_D7_30min_chr11_peaks.narrowPeak: No such file or directory
cat: GATA1_D7_30min_chr11_summits.bed: No such file or directory
[info] Get randomized [1000] peaks from the top [2000] peaks...
[info] Filtering the blacklist regions for the selected peak files
[info] Getting Fasta sequences
[info] Start MEME analysis for de novo motif finding ...
[info] Up to 10 will be output ...
Log::Log4perl configuration looks suspicious: No loggers defined at /Users/shivanikushwaha/opt/anaconda3/envs/meme/lib/site_perl/5.26.2/Log/Log4perl/Config.pm line 325.
Starting getsize: getsize random1000/MEME_GATA1_D7_30min_chr11_shuf/GATA1_D7_30min_chr11_summits_padded.fa 1> $metrics
getsize ran successfully in 0.026079 seconds
Starting fasta-most: fasta-most -min 50 < random1000/MEME_GATA1_D7_30min_chr11_shuf/GATA1_D7_30min_chr11_summits_padded.fa 1> $metrics
fasta-most ran successfully in 0.074794 seconds
Starting fasta-center: fasta-center -dna -len 100 < random1000/MEME_GATA1_D7_30min_chr11_shuf/GATA1_D7_30min_chr11_summits_padded.fa 1> random1000/MEME_GATA1_D7_30min_chr11_shuf/seqs-centered
fasta-center ran successfully in 0.081879 seconds
Starting fasta-shuffle-letters: fasta-shuffle-letters random1000/MEME_GATA1_D7_30min_chr11_shuf/seqs-centered random1000/MEME_GATA1_D7_30min_chr11_shuf/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
fasta-shuffle-letters ran successfully in 0.025716 seconds
Starting fasta-get-markov: fasta-get-markov -nostatus -nosummary -dna -m 1 random1000/MEME_GATA1_D7_30min_chr11_shuf/GATA1_D7_30min_chr11_summits_padded.fa random1000/MEME_GATA1_D7_30min_chr11_shuf/background
fasta-get-markov ran successfully in 0.024623 seconds
Starting meme: meme random1000/MEME_GATA1_D7_30min_chr11_shuf/seqs-centered -oc random1000/MEME_GATA1_D7_30min_chr11_shuf/meme_out -mod zoops -nmotifs 10 -minw 6 -maxw 30 -bfile random1000/MEME_GATA1_D7_30min_chr11_shuf/background -dna -revcomp -nostatus
No sequences found in file `random1000/MEME_GATA1_D7_30min_chr11_shuf/seqs-centered'. Check file format.
meme exited with error code 1
Starting dreme: dreme -verbosity 1 -oc random1000/MEME_GATA1_D7_30min_chr11_shuf/dreme_out -png -dna -p random1000/MEME_GATA1_D7_30min_chr11_shuf/seqs-centered -n random1000/MEME_GATA1_D7_30min_chr11_shuf/seqs-shuffled -m 10
File "/Users/shivanikushwaha/opt/anaconda3/envs/meme/bin/dreme", line 765
print "Finding secondary RE in left flank..."
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Finding secondary RE in left flank...")?
dreme exited with error code 1
Starting meme-chip_html_to_tsv: meme-chip_html_to_tsv random1000/MEME_GATA1_D7_30min_chr11_shuf/meme-chip.html random1000/MEME_GATA1_D7_30min_chr11_shuf/summary.tsv "meme-chip -oc random1000/MEME_GATA1_D7_30min_chr11_shuf -dreme-m 10 -meme-nmotifs 10 random1000/padded.fa/GATA1_D7_30min_chr11_summits_padded.fa" 5.0.5 "Mon Mar 18 20:12:19 2019 -0700"
meme-chip_html_to_tsv ran successfully in 0.132533 seconds
[info] De Novo motifs can be found: random1000/MEME_GATA1_D7_30min_chr11_shuf ...
[info] Loading the De Novo motifs ...
Traceback (most recent call last):
File "/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/install/read.meme.py", line 94, in
dreme_matrices = read_dreme(this_dir + "/dreme_out/dreme.txt")
File "/Users/shivanikushwaha/Documents/Documents_Shivani/apps/CUT-RUNTools-2.0/install/read.meme.py", line 47, in read_dreme
f = open(n)
FileNotFoundError: [Errno 2] No such file or directory: 'random1000/MEME_GATA1_D7_30min_chr11_shuf/dreme_out/dreme.txt'
[info] The signficance cutoff of Fimo scaning is 0.0005...
[info] Motif files can be found: random1000/MEME_GATA1_D7_30min_chr11_shuf/motifs
[info] Filtering the blacklist regions for the selected peak files
[info] Getting Fasta sequences
[info] Scaning the De Novo motifs for each peak
ls: random1000/MEME_GATA1_D7_30min_chr11_shuf/motifs: No such file or directory
[info] Output can be found: fimo.result/GATA1_D7_30min_chr11

Congrats! The bulk data analysis is complete!