Job ID = 6529095 SRX = SRX1078722 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: 00:06:56 27945127 reads; of these: 27945127 (100.00%) were unpaired; of these: 370587 (1.33%) aligned 0 times 23236939 (83.15%) aligned exactly 1 time 4337601 (15.52%) aligned >1 times 98.67% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 4042627 / 27574540 = 0.1466 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, 30 Jun 2020 01:36:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.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, 30 Jun 2020 01:36:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:36:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:36:14: 1000000 INFO @ Tue, 30 Jun 2020 01:36:20: 2000000 INFO @ Tue, 30 Jun 2020 01:36:26: 3000000 INFO @ Tue, 30 Jun 2020 01:36:31: 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, 30 Jun 2020 01:36:37: 5000000 INFO @ Tue, 30 Jun 2020 01:36:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.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, 30 Jun 2020 01:36:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:36:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:36:43: 6000000 INFO @ Tue, 30 Jun 2020 01:36:45: 1000000 INFO @ Tue, 30 Jun 2020 01:36:49: 7000000 INFO @ Tue, 30 Jun 2020 01:36:50: 2000000 INFO @ Tue, 30 Jun 2020 01:36:55: 8000000 INFO @ Tue, 30 Jun 2020 01:36:56: 3000000 INFO @ Tue, 30 Jun 2020 01:37:01: 9000000 INFO @ Tue, 30 Jun 2020 01:37:01: 4000000 INFO @ Tue, 30 Jun 2020 01:37:06: 10000000 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, 30 Jun 2020 01:37:07: 5000000 INFO @ Tue, 30 Jun 2020 01:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.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, 30 Jun 2020 01:37:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:37:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:37:12: 11000000 INFO @ Tue, 30 Jun 2020 01:37:13: 6000000 INFO @ Tue, 30 Jun 2020 01:37:15: 1000000 INFO @ Tue, 30 Jun 2020 01:37:18: 12000000 INFO @ Tue, 30 Jun 2020 01:37:19: 7000000 INFO @ Tue, 30 Jun 2020 01:37:21: 2000000 INFO @ Tue, 30 Jun 2020 01:37:24: 13000000 INFO @ Tue, 30 Jun 2020 01:37:25: 8000000 INFO @ Tue, 30 Jun 2020 01:37:26: 3000000 INFO @ Tue, 30 Jun 2020 01:37:30: 14000000 INFO @ Tue, 30 Jun 2020 01:37:30: 9000000 INFO @ Tue, 30 Jun 2020 01:37:32: 4000000 INFO @ Tue, 30 Jun 2020 01:37:35: 15000000 INFO @ Tue, 30 Jun 2020 01:37:36: 10000000 INFO @ Tue, 30 Jun 2020 01:37:38: 5000000 INFO @ Tue, 30 Jun 2020 01:37:41: 16000000 INFO @ Tue, 30 Jun 2020 01:37:42: 11000000 INFO @ Tue, 30 Jun 2020 01:37:44: 6000000 INFO @ Tue, 30 Jun 2020 01:37:47: 17000000 INFO @ Tue, 30 Jun 2020 01:37:47: 12000000 INFO @ Tue, 30 Jun 2020 01:37:50: 7000000 INFO @ Tue, 30 Jun 2020 01:37:53: 18000000 INFO @ Tue, 30 Jun 2020 01:37:53: 13000000 INFO @ Tue, 30 Jun 2020 01:37:56: 8000000 INFO @ Tue, 30 Jun 2020 01:37:59: 19000000 INFO @ Tue, 30 Jun 2020 01:37:59: 14000000 INFO @ Tue, 30 Jun 2020 01:38:02: 9000000 INFO @ Tue, 30 Jun 2020 01:38:04: 20000000 INFO @ Tue, 30 Jun 2020 01:38:05: 15000000 INFO @ Tue, 30 Jun 2020 01:38:07: 10000000 INFO @ Tue, 30 Jun 2020 01:38:10: 21000000 INFO @ Tue, 30 Jun 2020 01:38:11: 16000000 INFO @ Tue, 30 Jun 2020 01:38:13: 11000000 INFO @ Tue, 30 Jun 2020 01:38:16: 22000000 INFO @ Tue, 30 Jun 2020 01:38:16: 17000000 INFO @ Tue, 30 Jun 2020 01:38:19: 12000000 INFO @ Tue, 30 Jun 2020 01:38:22: 23000000 INFO @ Tue, 30 Jun 2020 01:38:22: 18000000 INFO @ Tue, 30 Jun 2020 01:38:25: 13000000 INFO @ Tue, 30 Jun 2020 01:38:25: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:38:25: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:38:25: #1 total tags in treatment: 23531913 INFO @ Tue, 30 Jun 2020 01:38:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:38:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:38:26: #1 tags after filtering in treatment: 23531913 INFO @ Tue, 30 Jun 2020 01:38:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:38:26: #1 finished! INFO @ Tue, 30 Jun 2020 01:38:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:38:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:38:27: #2 number of paired peaks: 163 WARNING @ Tue, 30 Jun 2020 01:38:27: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 30 Jun 2020 01:38:27: start model_add_line... INFO @ Tue, 30 Jun 2020 01:38:28: start X-correlation... INFO @ Tue, 30 Jun 2020 01:38:28: end of X-cor INFO @ Tue, 30 Jun 2020 01:38:28: #2 finished! INFO @ Tue, 30 Jun 2020 01:38:28: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:38:28: #2 alternative fragment length(s) may be 1,13,34,545 bps INFO @ Tue, 30 Jun 2020 01:38:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.05_model.r WARNING @ Tue, 30 Jun 2020 01:38:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:38:28: #2 You may need to consider one of the other alternative d(s): 1,13,34,545 WARNING @ Tue, 30 Jun 2020 01:38:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:38:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:38:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:38:28: 19000000 INFO @ Tue, 30 Jun 2020 01:38:31: 14000000 INFO @ Tue, 30 Jun 2020 01:38:34: 20000000 INFO @ Tue, 30 Jun 2020 01:38:36: 15000000 INFO @ Tue, 30 Jun 2020 01:38:40: 21000000 INFO @ Tue, 30 Jun 2020 01:38:42: 16000000 INFO @ Tue, 30 Jun 2020 01:38:45: 22000000 INFO @ Tue, 30 Jun 2020 01:38:48: 17000000 INFO @ Tue, 30 Jun 2020 01:38:51: 23000000 INFO @ Tue, 30 Jun 2020 01:38:54: 18000000 INFO @ Tue, 30 Jun 2020 01:38:54: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:38:54: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:38:54: #1 total tags in treatment: 23531913 INFO @ Tue, 30 Jun 2020 01:38:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:38:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:38:55: #1 tags after filtering in treatment: 23531913 INFO @ Tue, 30 Jun 2020 01:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:38:55: #1 finished! INFO @ Tue, 30 Jun 2020 01:38:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:38:57: #2 number of paired peaks: 163 WARNING @ Tue, 30 Jun 2020 01:38:57: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 30 Jun 2020 01:38:57: start model_add_line... INFO @ Tue, 30 Jun 2020 01:38:57: start X-correlation... INFO @ Tue, 30 Jun 2020 01:38:57: end of X-cor INFO @ Tue, 30 Jun 2020 01:38:57: #2 finished! INFO @ Tue, 30 Jun 2020 01:38:57: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:38:57: #2 alternative fragment length(s) may be 1,13,34,545 bps INFO @ Tue, 30 Jun 2020 01:38:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.10_model.r WARNING @ Tue, 30 Jun 2020 01:38:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:38:57: #2 You may need to consider one of the other alternative d(s): 1,13,34,545 WARNING @ Tue, 30 Jun 2020 01:38:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:38:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:38:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:39:00: 19000000 INFO @ Tue, 30 Jun 2020 01:39:05: 20000000 INFO @ Tue, 30 Jun 2020 01:39:08: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:39:11: 21000000 INFO @ Tue, 30 Jun 2020 01:39:17: 22000000 INFO @ Tue, 30 Jun 2020 01:39:23: 23000000 INFO @ Tue, 30 Jun 2020 01:39:26: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:39:26: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:39:26: #1 total tags in treatment: 23531913 INFO @ Tue, 30 Jun 2020 01:39:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:39:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:39:26: #1 tags after filtering in treatment: 23531913 INFO @ Tue, 30 Jun 2020 01:39:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:39:26: #1 finished! INFO @ Tue, 30 Jun 2020 01:39:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:39:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:39:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:39:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:39:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.05_summits.bed INFO @ Tue, 30 Jun 2020 01:39:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:39:28: #2 number of paired peaks: 163 WARNING @ Tue, 30 Jun 2020 01:39:28: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 30 Jun 2020 01:39:28: start model_add_line... INFO @ Tue, 30 Jun 2020 01:39:28: start X-correlation... INFO @ Tue, 30 Jun 2020 01:39:29: end of X-cor INFO @ Tue, 30 Jun 2020 01:39:29: #2 finished! INFO @ Tue, 30 Jun 2020 01:39:29: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:39:29: #2 alternative fragment length(s) may be 1,13,34,545 bps INFO @ Tue, 30 Jun 2020 01:39:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.20_model.r WARNING @ Tue, 30 Jun 2020 01:39:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:39:29: #2 You may need to consider one of the other alternative d(s): 1,13,34,545 WARNING @ Tue, 30 Jun 2020 01:39:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:39:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:39:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:39:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:39:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.10_summits.bed INFO @ Tue, 30 Jun 2020 01:39:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:40:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:40:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:40:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:40:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078722/SRX1078722.20_summits.bed INFO @ Tue, 30 Jun 2020 01:40:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling