Job ID = 6367493 SRX = SRX331250 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:47:59 prefetch.2.10.7: 1) Downloading 'SRR947482'... 2020-06-15T23:47:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:55 prefetch.2.10.7: 'SRR947482' is valid 2020-06-15T23:48:55 prefetch.2.10.7: 1) 'SRR947482' was downloaded successfully Read 7662619 spots for SRR947482/SRR947482.sra Written 7662619 spots for SRR947482/SRR947482.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:16 7662619 reads; of these: 7662619 (100.00%) were unpaired; of these: 3126186 (40.80%) aligned 0 times 3743777 (48.86%) aligned exactly 1 time 792656 (10.34%) aligned >1 times 59.20% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 408937 / 4536433 = 0.0901 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:52:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:52:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:21: 1000000 INFO @ Tue, 16 Jun 2020 08:52:28: 2000000 INFO @ Tue, 16 Jun 2020 08:52:35: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:52:42: 4000000 INFO @ Tue, 16 Jun 2020 08:52:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:52:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:52:43: #1 total tags in treatment: 4127496 INFO @ Tue, 16 Jun 2020 08:52:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:52:43: #1 tags after filtering in treatment: 4127496 INFO @ Tue, 16 Jun 2020 08:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:52:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:52:43: #2 number of paired peaks: 572 WARNING @ Tue, 16 Jun 2020 08:52:43: Fewer paired peaks (572) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 572 pairs to build model! INFO @ Tue, 16 Jun 2020 08:52:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:52:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:52:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:52:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:52:43: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:52:43: #2 alternative fragment length(s) may be 3,35,86,575 bps INFO @ Tue, 16 Jun 2020 08:52:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.05_model.r WARNING @ Tue, 16 Jun 2020 08:52:43: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:52:43: #2 You may need to consider one of the other alternative d(s): 3,35,86,575 WARNING @ Tue, 16 Jun 2020 08:52:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:52:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:52:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:52:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:52: 1000000 INFO @ Tue, 16 Jun 2020 08:52:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.05_summits.bed INFO @ Tue, 16 Jun 2020 08:52:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (577 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:53:00: 2000000 INFO @ Tue, 16 Jun 2020 08:53:08: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:53:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:15: 4000000 INFO @ Tue, 16 Jun 2020 08:53:16: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:53:16: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:53:16: #1 total tags in treatment: 4127496 INFO @ Tue, 16 Jun 2020 08:53:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:53:16: #1 tags after filtering in treatment: 4127496 INFO @ Tue, 16 Jun 2020 08:53:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:53:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:16: #2 number of paired peaks: 572 WARNING @ Tue, 16 Jun 2020 08:53:16: Fewer paired peaks (572) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 572 pairs to build model! INFO @ Tue, 16 Jun 2020 08:53:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:16: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:53:16: #2 alternative fragment length(s) may be 3,35,86,575 bps INFO @ Tue, 16 Jun 2020 08:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.10_model.r WARNING @ Tue, 16 Jun 2020 08:53:16: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:53:16: #2 You may need to consider one of the other alternative d(s): 3,35,86,575 WARNING @ Tue, 16 Jun 2020 08:53:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:53:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:53:22: 1000000 INFO @ Tue, 16 Jun 2020 08:53:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.10_summits.bed INFO @ Tue, 16 Jun 2020 08:53:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (252 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:53:30: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:53:37: 3000000 INFO @ Tue, 16 Jun 2020 08:53:45: 4000000 INFO @ Tue, 16 Jun 2020 08:53:45: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:53:45: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:53:45: #1 total tags in treatment: 4127496 INFO @ Tue, 16 Jun 2020 08:53:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:53:45: #1 tags after filtering in treatment: 4127496 INFO @ Tue, 16 Jun 2020 08:53:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:53:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:46: #2 number of paired peaks: 572 WARNING @ Tue, 16 Jun 2020 08:53:46: Fewer paired peaks (572) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 572 pairs to build model! INFO @ Tue, 16 Jun 2020 08:53:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:46: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:53:46: #2 alternative fragment length(s) may be 3,35,86,575 bps INFO @ Tue, 16 Jun 2020 08:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.20_model.r WARNING @ Tue, 16 Jun 2020 08:53:46: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:53:46: #2 You may need to consider one of the other alternative d(s): 3,35,86,575 WARNING @ Tue, 16 Jun 2020 08:53:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:53:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:53:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331250/SRX331250.20_summits.bed INFO @ Tue, 16 Jun 2020 08:53:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 1 millis CompletedMACS2peakCalling