Job ID = 6626602 SRX = SRX7630547 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:05:30 31885727 reads; of these: 31885727 (100.00%) were unpaired; of these: 10815871 (33.92%) aligned 0 times 17606611 (55.22%) aligned exactly 1 time 3463245 (10.86%) aligned >1 times 66.08% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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 12 files... [bam_rmdupse_core] 7932541 / 21069856 = 0.3765 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, 14 Jul 2020 07:59:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.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, 14 Jul 2020 07:59:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:59:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:59:18: 1000000 INFO @ Tue, 14 Jul 2020 07:59:23: 2000000 INFO @ Tue, 14 Jul 2020 07:59:28: 3000000 INFO @ Tue, 14 Jul 2020 07:59:34: 4000000 INFO @ Tue, 14 Jul 2020 07:59:39: 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, 14 Jul 2020 07:59:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.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, 14 Jul 2020 07:59:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:59:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:59:44: 6000000 INFO @ Tue, 14 Jul 2020 07:59:48: 1000000 INFO @ Tue, 14 Jul 2020 07:59:50: 7000000 INFO @ Tue, 14 Jul 2020 07:59:53: 2000000 INFO @ Tue, 14 Jul 2020 07:59:55: 8000000 INFO @ Tue, 14 Jul 2020 07:59:59: 3000000 INFO @ Tue, 14 Jul 2020 08:00:01: 9000000 INFO @ Tue, 14 Jul 2020 08:00:04: 4000000 INFO @ Tue, 14 Jul 2020 08:00:06: 10000000 INFO @ Tue, 14 Jul 2020 08:00:09: 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, 14 Jul 2020 08:00:11: 11000000 INFO @ Tue, 14 Jul 2020 08:00:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.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, 14 Jul 2020 08:00:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:00:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:00:15: 6000000 INFO @ Tue, 14 Jul 2020 08:00:17: 12000000 INFO @ Tue, 14 Jul 2020 08:00:18: 1000000 INFO @ Tue, 14 Jul 2020 08:00:20: 7000000 INFO @ Tue, 14 Jul 2020 08:00:22: 13000000 INFO @ Tue, 14 Jul 2020 08:00:23: 2000000 INFO @ Tue, 14 Jul 2020 08:00:23: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:00:23: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:00:23: #1 total tags in treatment: 13137315 INFO @ Tue, 14 Jul 2020 08:00:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:00:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:00:23: #1 tags after filtering in treatment: 13137315 INFO @ Tue, 14 Jul 2020 08:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:00:23: #1 finished! INFO @ Tue, 14 Jul 2020 08:00:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:00:24: #2 number of paired peaks: 326 WARNING @ Tue, 14 Jul 2020 08:00:24: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 14 Jul 2020 08:00:24: start model_add_line... INFO @ Tue, 14 Jul 2020 08:00:24: start X-correlation... INFO @ Tue, 14 Jul 2020 08:00:24: end of X-cor INFO @ Tue, 14 Jul 2020 08:00:24: #2 finished! INFO @ Tue, 14 Jul 2020 08:00:24: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 08:00:24: #2 alternative fragment length(s) may be 2,37 bps INFO @ Tue, 14 Jul 2020 08:00:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.05_model.r WARNING @ Tue, 14 Jul 2020 08:00:24: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:00:24: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Tue, 14 Jul 2020 08:00:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:00:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:00:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:00:26: 8000000 INFO @ Tue, 14 Jul 2020 08:00:28: 3000000 INFO @ Tue, 14 Jul 2020 08:00:31: 9000000 INFO @ Tue, 14 Jul 2020 08:00:33: 4000000 INFO @ Tue, 14 Jul 2020 08:00:37: 10000000 INFO @ Tue, 14 Jul 2020 08:00:38: 5000000 INFO @ Tue, 14 Jul 2020 08:00:42: 11000000 INFO @ Tue, 14 Jul 2020 08:00:43: 6000000 INFO @ Tue, 14 Jul 2020 08:00:47: 12000000 INFO @ Tue, 14 Jul 2020 08:00:48: 7000000 INFO @ Tue, 14 Jul 2020 08:00:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:00:52: 8000000 INFO @ Tue, 14 Jul 2020 08:00:53: 13000000 INFO @ Tue, 14 Jul 2020 08:00:54: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:00:54: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:00:54: #1 total tags in treatment: 13137315 INFO @ Tue, 14 Jul 2020 08:00:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:00:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:00:54: #1 tags after filtering in treatment: 13137315 INFO @ Tue, 14 Jul 2020 08:00:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:00:54: #1 finished! INFO @ Tue, 14 Jul 2020 08:00:54: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:00:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:00:55: #2 number of paired peaks: 326 WARNING @ Tue, 14 Jul 2020 08:00:55: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 14 Jul 2020 08:00:55: start model_add_line... INFO @ Tue, 14 Jul 2020 08:00:55: start X-correlation... INFO @ Tue, 14 Jul 2020 08:00:55: end of X-cor INFO @ Tue, 14 Jul 2020 08:00:55: #2 finished! INFO @ Tue, 14 Jul 2020 08:00:55: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 08:00:55: #2 alternative fragment length(s) may be 2,37 bps INFO @ Tue, 14 Jul 2020 08:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.10_model.r WARNING @ Tue, 14 Jul 2020 08:00:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:00:55: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Tue, 14 Jul 2020 08:00:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:00:55: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:00:57: 9000000 INFO @ Tue, 14 Jul 2020 08:00:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:00:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:00:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.05_summits.bed INFO @ Tue, 14 Jul 2020 08:00:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:01:02: 10000000 INFO @ Tue, 14 Jul 2020 08:01:07: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:01:11: 12000000 INFO @ Tue, 14 Jul 2020 08:01:16: 13000000 INFO @ Tue, 14 Jul 2020 08:01:17: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:01:17: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:01:17: #1 total tags in treatment: 13137315 INFO @ Tue, 14 Jul 2020 08:01:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:01:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:01:17: #1 tags after filtering in treatment: 13137315 INFO @ Tue, 14 Jul 2020 08:01:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:01:17: #1 finished! INFO @ Tue, 14 Jul 2020 08:01:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:01:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:01:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:01:18: #2 number of paired peaks: 326 WARNING @ Tue, 14 Jul 2020 08:01:18: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 14 Jul 2020 08:01:18: start model_add_line... INFO @ Tue, 14 Jul 2020 08:01:18: start X-correlation... INFO @ Tue, 14 Jul 2020 08:01:18: end of X-cor INFO @ Tue, 14 Jul 2020 08:01:18: #2 finished! INFO @ Tue, 14 Jul 2020 08:01:18: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 08:01:18: #2 alternative fragment length(s) may be 2,37 bps INFO @ Tue, 14 Jul 2020 08:01:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.20_model.r WARNING @ Tue, 14 Jul 2020 08:01:18: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:01:18: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Tue, 14 Jul 2020 08:01:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:01:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:01:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:01:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:01:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:01:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.10_summits.bed INFO @ Tue, 14 Jul 2020 08:01:29: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:01:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630547/SRX7630547.20_summits.bed INFO @ Tue, 14 Jul 2020 08:01:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling