Job ID = 6366566 SRX = SRX1936244 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:11 prefetch.2.10.7: 1) Downloading 'SRR3879851'... 2020-06-15T22:54:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:24 prefetch.2.10.7: 1) 'SRR3879851' was downloaded successfully Read 21274743 spots for SRR3879851/SRR3879851.sra Written 21274743 spots for SRR3879851/SRR3879851.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: 00:04:30 21274743 reads; of these: 21274743 (100.00%) were unpaired; of these: 3316607 (15.59%) aligned 0 times 14919183 (70.13%) aligned exactly 1 time 3038953 (14.28%) aligned >1 times 84.41% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2354821 / 17958136 = 0.1311 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 08:06:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.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 08:06:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:24: 1000000 INFO @ Tue, 16 Jun 2020 08:06:29: 2000000 INFO @ Tue, 16 Jun 2020 08:06:34: 3000000 INFO @ Tue, 16 Jun 2020 08:06:40: 4000000 INFO @ Tue, 16 Jun 2020 08:06:45: 5000000 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 08:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.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 08:06:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:50: 6000000 INFO @ Tue, 16 Jun 2020 08:06:56: 1000000 INFO @ Tue, 16 Jun 2020 08:06:57: 7000000 INFO @ Tue, 16 Jun 2020 08:07:03: 2000000 INFO @ Tue, 16 Jun 2020 08:07:03: 8000000 INFO @ Tue, 16 Jun 2020 08:07:09: 9000000 INFO @ Tue, 16 Jun 2020 08:07:10: 3000000 INFO @ Tue, 16 Jun 2020 08:07:15: 10000000 INFO @ Tue, 16 Jun 2020 08:07:17: 4000000 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 08:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.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 08:07:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:22: 11000000 INFO @ Tue, 16 Jun 2020 08:07:24: 5000000 INFO @ Tue, 16 Jun 2020 08:07:25: 1000000 INFO @ Tue, 16 Jun 2020 08:07:28: 12000000 INFO @ Tue, 16 Jun 2020 08:07:31: 6000000 INFO @ Tue, 16 Jun 2020 08:07:31: 2000000 INFO @ Tue, 16 Jun 2020 08:07:35: 13000000 INFO @ Tue, 16 Jun 2020 08:07:38: 7000000 INFO @ Tue, 16 Jun 2020 08:07:38: 3000000 INFO @ Tue, 16 Jun 2020 08:07:41: 14000000 INFO @ Tue, 16 Jun 2020 08:07:44: 4000000 INFO @ Tue, 16 Jun 2020 08:07:45: 8000000 INFO @ Tue, 16 Jun 2020 08:07:48: 15000000 INFO @ Tue, 16 Jun 2020 08:07:51: 5000000 INFO @ Tue, 16 Jun 2020 08:07:51: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:07:51: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:07:51: #1 total tags in treatment: 15603315 INFO @ Tue, 16 Jun 2020 08:07:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:51: #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 08:07:52: 9000000 INFO @ Tue, 16 Jun 2020 08:07:52: #1 tags after filtering in treatment: 15603315 INFO @ Tue, 16 Jun 2020 08:07:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:53: #2 number of paired peaks: 258 WARNING @ Tue, 16 Jun 2020 08:07:53: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:53: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:07:53: #2 alternative fragment length(s) may be 1,47,549,563,595 bps INFO @ Tue, 16 Jun 2020 08:07:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.05_model.r WARNING @ Tue, 16 Jun 2020 08:07:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:53: #2 You may need to consider one of the other alternative d(s): 1,47,549,563,595 WARNING @ Tue, 16 Jun 2020 08:07:53: #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 08:07:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:57: 6000000 INFO @ Tue, 16 Jun 2020 08:07:59: 10000000 INFO @ Tue, 16 Jun 2020 08:08:03: 7000000 INFO @ Tue, 16 Jun 2020 08:08:06: 11000000 INFO @ Tue, 16 Jun 2020 08:08:09: 8000000 INFO @ Tue, 16 Jun 2020 08:08:13: 12000000 INFO @ Tue, 16 Jun 2020 08:08:15: 9000000 INFO @ Tue, 16 Jun 2020 08:08:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:20: 13000000 INFO @ Tue, 16 Jun 2020 08:08:22: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:27: 14000000 INFO @ Tue, 16 Jun 2020 08:08:28: 11000000 INFO @ Tue, 16 Jun 2020 08:08:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (672 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:34: 12000000 INFO @ Tue, 16 Jun 2020 08:08:35: 15000000 INFO @ Tue, 16 Jun 2020 08:08:39: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:08:39: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:08:39: #1 total tags in treatment: 15603315 INFO @ Tue, 16 Jun 2020 08:08:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:39: #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 08:08:39: #1 tags after filtering in treatment: 15603315 INFO @ Tue, 16 Jun 2020 08:08:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:40: 13000000 INFO @ Tue, 16 Jun 2020 08:08:40: #2 number of paired peaks: 258 WARNING @ Tue, 16 Jun 2020 08:08:40: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:40: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:08:40: #2 alternative fragment length(s) may be 1,47,549,563,595 bps INFO @ Tue, 16 Jun 2020 08:08:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.10_model.r WARNING @ Tue, 16 Jun 2020 08:08:40: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:40: #2 You may need to consider one of the other alternative d(s): 1,47,549,563,595 WARNING @ Tue, 16 Jun 2020 08:08:40: #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 08:08:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:46: 14000000 INFO @ Tue, 16 Jun 2020 08:08:51: 15000000 INFO @ Tue, 16 Jun 2020 08:08:54: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:08:54: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:08:54: #1 total tags in treatment: 15603315 INFO @ Tue, 16 Jun 2020 08:08:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:54: #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 08:08:55: #1 tags after filtering in treatment: 15603315 INFO @ Tue, 16 Jun 2020 08:08:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:56: #2 number of paired peaks: 258 WARNING @ Tue, 16 Jun 2020 08:08:56: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:56: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:08:56: #2 alternative fragment length(s) may be 1,47,549,563,595 bps INFO @ Tue, 16 Jun 2020 08:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.20_model.r WARNING @ Tue, 16 Jun 2020 08:08:56: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:56: #2 You may need to consider one of the other alternative d(s): 1,47,549,563,595 WARNING @ Tue, 16 Jun 2020 08:08:56: #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 08:08:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.10_summits.bed INFO @ Tue, 16 Jun 2020 08:09:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (435 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936244/SRX1936244.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 1 millis CompletedMACS2peakCalling