Job ID = 6366323 SRX = SRX1132919 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:42:23 prefetch.2.10.7: 1) Downloading 'SRR2144368'... 2020-06-15T22:42:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:31 prefetch.2.10.7: 'SRR2144368' is valid 2020-06-15T22:43:31 prefetch.2.10.7: 1) 'SRR2144368' was downloaded successfully Read 12232138 spots for SRR2144368/SRR2144368.sra Written 12232138 spots for SRR2144368/SRR2144368.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: 00:03:39 12232138 reads; of these: 12232138 (100.00%) were unpaired; of these: 1127209 (9.22%) aligned 0 times 9191434 (75.14%) aligned exactly 1 time 1913495 (15.64%) aligned >1 times 90.78% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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] 2924231 / 11104929 = 0.2633 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 07:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.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 07:51:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:46: 1000000 INFO @ Tue, 16 Jun 2020 07:51:52: 2000000 INFO @ Tue, 16 Jun 2020 07:51:58: 3000000 INFO @ Tue, 16 Jun 2020 07:52:04: 4000000 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 07:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.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 07:52:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:10: 5000000 INFO @ Tue, 16 Jun 2020 07:52:15: 1000000 INFO @ Tue, 16 Jun 2020 07:52:17: 6000000 INFO @ Tue, 16 Jun 2020 07:52:21: 2000000 INFO @ Tue, 16 Jun 2020 07:52:23: 7000000 INFO @ Tue, 16 Jun 2020 07:52:26: 3000000 INFO @ Tue, 16 Jun 2020 07:52:29: 8000000 INFO @ Tue, 16 Jun 2020 07:52:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:52:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:52:30: #1 total tags in treatment: 8180698 INFO @ Tue, 16 Jun 2020 07:52:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:30: #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 07:52:31: #1 tags after filtering in treatment: 8180698 INFO @ Tue, 16 Jun 2020 07:52:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:31: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:31: #2 number of paired peaks: 270 WARNING @ Tue, 16 Jun 2020 07:52:31: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:31: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:31: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:31: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:31: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:31: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 07:52:31: #2 alternative fragment length(s) may be 2,49,535,567 bps INFO @ Tue, 16 Jun 2020 07:52:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.05_model.r WARNING @ Tue, 16 Jun 2020 07:52:31: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:31: #2 You may need to consider one of the other alternative d(s): 2,49,535,567 WARNING @ Tue, 16 Jun 2020 07:52:31: #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 07:52:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:32: 4000000 INFO @ Tue, 16 Jun 2020 07:52:38: 5000000 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 07:52:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.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 07:52:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:43: 6000000 INFO @ Tue, 16 Jun 2020 07:52:46: 1000000 INFO @ Tue, 16 Jun 2020 07:52:49: 7000000 INFO @ Tue, 16 Jun 2020 07:52:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:51: 2000000 INFO @ Tue, 16 Jun 2020 07:52:55: 8000000 INFO @ Tue, 16 Jun 2020 07:52:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:52:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:52:56: #1 total tags in treatment: 8180698 INFO @ Tue, 16 Jun 2020 07:52:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:56: #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 07:52:56: #1 tags after filtering in treatment: 8180698 INFO @ Tue, 16 Jun 2020 07:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:56: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:56: #2 number of paired peaks: 270 WARNING @ Tue, 16 Jun 2020 07:52:56: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:56: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 07:52:56: #2 alternative fragment length(s) may be 2,49,535,567 bps INFO @ Tue, 16 Jun 2020 07:52:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.10_model.r WARNING @ Tue, 16 Jun 2020 07:52:56: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:56: #2 You may need to consider one of the other alternative d(s): 2,49,535,567 WARNING @ Tue, 16 Jun 2020 07:52:56: #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 07:52:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:57: 3000000 INFO @ Tue, 16 Jun 2020 07:52:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.05_summits.bed INFO @ Tue, 16 Jun 2020 07:52:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (673 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:02: 4000000 INFO @ Tue, 16 Jun 2020 07:53:08: 5000000 INFO @ Tue, 16 Jun 2020 07:53:14: 6000000 INFO @ Tue, 16 Jun 2020 07:53:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:19: 7000000 INFO @ Tue, 16 Jun 2020 07:53:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.10_summits.bed INFO @ Tue, 16 Jun 2020 07:53:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (195 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:25: 8000000 INFO @ Tue, 16 Jun 2020 07:53:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:53:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:53:26: #1 total tags in treatment: 8180698 INFO @ Tue, 16 Jun 2020 07:53:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:26: #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 07:53:26: #1 tags after filtering in treatment: 8180698 INFO @ Tue, 16 Jun 2020 07:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:27: #2 number of paired peaks: 270 WARNING @ Tue, 16 Jun 2020 07:53:27: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:27: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:27: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:27: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:27: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:27: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 07:53:27: #2 alternative fragment length(s) may be 2,49,535,567 bps INFO @ Tue, 16 Jun 2020 07:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.20_model.r WARNING @ Tue, 16 Jun 2020 07:53:27: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:27: #2 You may need to consider one of the other alternative d(s): 2,49,535,567 WARNING @ Tue, 16 Jun 2020 07:53:27: #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 07:53:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:27: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:53:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:53:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1132919/SRX1132919.20_summits.bed INFO @ Tue, 16 Jun 2020 07:53:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (43 records, 4 fields): 1 millis CompletedMACS2peakCalling