Job ID = 6497373 SRX = SRX331184 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:34:20 prefetch.2.10.7: 1) Downloading 'SRR947416'... 2020-06-25T22:34:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:34:58 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:34:59 prefetch.2.10.7: 'SRR947416' is valid 2020-06-25T22:34:59 prefetch.2.10.7: 1) 'SRR947416' was downloaded successfully Read 5886071 spots for SRR947416/SRR947416.sra Written 5886071 spots for SRR947416/SRR947416.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: 00:00:57 5886071 reads; of these: 5886071 (100.00%) were unpaired; of these: 585857 (9.95%) aligned 0 times 4439740 (75.43%) aligned exactly 1 time 860474 (14.62%) aligned >1 times 90.05% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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] 593344 / 5300214 = 0.1119 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 @ Fri, 26 Jun 2020 07:37:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.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 @ Fri, 26 Jun 2020 07:37:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:37:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:37:51: 1000000 INFO @ Fri, 26 Jun 2020 07:37:56: 2000000 INFO @ Fri, 26 Jun 2020 07:38:01: 3000000 INFO @ Fri, 26 Jun 2020 07:38:07: 4000000 INFO @ Fri, 26 Jun 2020 07:38:10: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 07:38:10: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 07:38:10: #1 total tags in treatment: 4706870 INFO @ Fri, 26 Jun 2020 07:38:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:38:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:38:10: #1 tags after filtering in treatment: 4706870 INFO @ Fri, 26 Jun 2020 07:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:38:10: #1 finished! INFO @ Fri, 26 Jun 2020 07:38:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:38:11: #2 number of paired peaks: 441 WARNING @ Fri, 26 Jun 2020 07:38:11: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 26 Jun 2020 07:38:11: start model_add_line... INFO @ Fri, 26 Jun 2020 07:38:11: start X-correlation... INFO @ Fri, 26 Jun 2020 07:38:11: end of X-cor INFO @ Fri, 26 Jun 2020 07:38:11: #2 finished! INFO @ Fri, 26 Jun 2020 07:38:11: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 07:38:11: #2 alternative fragment length(s) may be 4,34,94,585 bps INFO @ Fri, 26 Jun 2020 07:38:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.05_model.r WARNING @ Fri, 26 Jun 2020 07:38:11: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:38:11: #2 You may need to consider one of the other alternative d(s): 4,34,94,585 WARNING @ Fri, 26 Jun 2020 07:38:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:38:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:38:11: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 07:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.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 @ Fri, 26 Jun 2020 07:38:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:38:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:38:21: 1000000 INFO @ Fri, 26 Jun 2020 07:38:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:38:27: 2000000 INFO @ Fri, 26 Jun 2020 07:38:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:38:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:38:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.05_summits.bed INFO @ Fri, 26 Jun 2020 07:38:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (552 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:38:32: 3000000 INFO @ Fri, 26 Jun 2020 07:38:37: 4000000 INFO @ Fri, 26 Jun 2020 07:38:41: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 07:38:41: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 07:38:41: #1 total tags in treatment: 4706870 INFO @ Fri, 26 Jun 2020 07:38:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:38:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:38:41: #1 tags after filtering in treatment: 4706870 INFO @ Fri, 26 Jun 2020 07:38:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:38:41: #1 finished! INFO @ Fri, 26 Jun 2020 07:38:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:38:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:38:41: #2 number of paired peaks: 441 WARNING @ Fri, 26 Jun 2020 07:38:41: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 26 Jun 2020 07:38:41: start model_add_line... INFO @ Fri, 26 Jun 2020 07:38:41: start X-correlation... INFO @ Fri, 26 Jun 2020 07:38:41: end of X-cor INFO @ Fri, 26 Jun 2020 07:38:41: #2 finished! INFO @ Fri, 26 Jun 2020 07:38:41: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 07:38:41: #2 alternative fragment length(s) may be 4,34,94,585 bps INFO @ Fri, 26 Jun 2020 07:38:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.10_model.r WARNING @ Fri, 26 Jun 2020 07:38:41: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:38:41: #2 You may need to consider one of the other alternative d(s): 4,34,94,585 WARNING @ Fri, 26 Jun 2020 07:38:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:38:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:38:41: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 07:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.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 @ Fri, 26 Jun 2020 07:38:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:38:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:38:52: 1000000 INFO @ Fri, 26 Jun 2020 07:38:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:38:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:38:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:38:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.10_summits.bed INFO @ Fri, 26 Jun 2020 07:38:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (242 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:38:58: 2000000 INFO @ Fri, 26 Jun 2020 07:39:03: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:39:09: 4000000 INFO @ Fri, 26 Jun 2020 07:39:12: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 07:39:12: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 07:39:12: #1 total tags in treatment: 4706870 INFO @ Fri, 26 Jun 2020 07:39:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:39:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:39:13: #1 tags after filtering in treatment: 4706870 INFO @ Fri, 26 Jun 2020 07:39:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:39:13: #1 finished! INFO @ Fri, 26 Jun 2020 07:39:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:39:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:39:13: #2 number of paired peaks: 441 WARNING @ Fri, 26 Jun 2020 07:39:13: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 26 Jun 2020 07:39:13: start model_add_line... INFO @ Fri, 26 Jun 2020 07:39:13: start X-correlation... INFO @ Fri, 26 Jun 2020 07:39:13: end of X-cor INFO @ Fri, 26 Jun 2020 07:39:13: #2 finished! INFO @ Fri, 26 Jun 2020 07:39:13: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 07:39:13: #2 alternative fragment length(s) may be 4,34,94,585 bps INFO @ Fri, 26 Jun 2020 07:39:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.20_model.r WARNING @ Fri, 26 Jun 2020 07:39:13: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:39:13: #2 You may need to consider one of the other alternative d(s): 4,34,94,585 WARNING @ Fri, 26 Jun 2020 07:39:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:39:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:39:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:39:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:39:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:39:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:39:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331184/SRX331184.20_summits.bed INFO @ Fri, 26 Jun 2020 07:39:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 1 millis CompletedMACS2peakCalling