Job ID = 10166080 SRX = SRX9120606 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: 00:07:32 37410483 reads; of these: 37410483 (100.00%) were unpaired; of these: 6038931 (16.14%) aligned 0 times 26041623 (69.61%) aligned exactly 1 time 5329929 (14.25%) aligned >1 times 83.86% overall alignment rate Time searching: 00:07:32 Overall time: 00:07:32 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 16 files... [bam_rmdupse_core] 6016113 / 31371552 = 0.1918 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 @ Thu, 08 Oct 2020 20:41:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.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 @ Thu, 08 Oct 2020 20:41:34: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:41:34: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:39: 1000000 INFO @ Thu, 08 Oct 2020 20:41:43: 2000000 INFO @ Thu, 08 Oct 2020 20:41:48: 3000000 INFO @ Thu, 08 Oct 2020 20:41:53: 4000000 INFO @ Thu, 08 Oct 2020 20:41:57: 5000000 INFO @ Thu, 08 Oct 2020 20:42:02: 6000000 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 @ Thu, 08 Oct 2020 20:42:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.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 @ Thu, 08 Oct 2020 20:42:04: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:42:04: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:42:07: 7000000 INFO @ Thu, 08 Oct 2020 20:42:09: 1000000 INFO @ Thu, 08 Oct 2020 20:42:12: 8000000 INFO @ Thu, 08 Oct 2020 20:42:14: 2000000 INFO @ Thu, 08 Oct 2020 20:42:16: 9000000 INFO @ Thu, 08 Oct 2020 20:42:19: 3000000 INFO @ Thu, 08 Oct 2020 20:42:21: 10000000 INFO @ Thu, 08 Oct 2020 20:42:23: 4000000 INFO @ Thu, 08 Oct 2020 20:42:26: 11000000 INFO @ Thu, 08 Oct 2020 20:42:28: 5000000 INFO @ Thu, 08 Oct 2020 20:42:31: 12000000 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 @ Thu, 08 Oct 2020 20:42:33: 6000000 INFO @ Thu, 08 Oct 2020 20:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.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 @ Thu, 08 Oct 2020 20:42:34: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:42:34: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:42:36: 13000000 INFO @ Thu, 08 Oct 2020 20:42:38: 7000000 INFO @ Thu, 08 Oct 2020 20:42:39: 1000000 INFO @ Thu, 08 Oct 2020 20:42:41: 14000000 INFO @ Thu, 08 Oct 2020 20:42:43: 8000000 INFO @ Thu, 08 Oct 2020 20:42:44: 2000000 INFO @ Thu, 08 Oct 2020 20:42:46: 15000000 INFO @ Thu, 08 Oct 2020 20:42:48: 9000000 INFO @ Thu, 08 Oct 2020 20:42:49: 3000000 INFO @ Thu, 08 Oct 2020 20:42:51: 16000000 INFO @ Thu, 08 Oct 2020 20:42:53: 10000000 INFO @ Thu, 08 Oct 2020 20:42:54: 4000000 INFO @ Thu, 08 Oct 2020 20:42:56: 17000000 INFO @ Thu, 08 Oct 2020 20:42:58: 11000000 INFO @ Thu, 08 Oct 2020 20:42:59: 5000000 INFO @ Thu, 08 Oct 2020 20:43:01: 18000000 INFO @ Thu, 08 Oct 2020 20:43:03: 12000000 INFO @ Thu, 08 Oct 2020 20:43:04: 6000000 INFO @ Thu, 08 Oct 2020 20:43:06: 19000000 INFO @ Thu, 08 Oct 2020 20:43:09: 13000000 INFO @ Thu, 08 Oct 2020 20:43:09: 7000000 INFO @ Thu, 08 Oct 2020 20:43:11: 20000000 INFO @ Thu, 08 Oct 2020 20:43:14: 14000000 INFO @ Thu, 08 Oct 2020 20:43:14: 8000000 INFO @ Thu, 08 Oct 2020 20:43:16: 21000000 INFO @ Thu, 08 Oct 2020 20:43:19: 15000000 INFO @ Thu, 08 Oct 2020 20:43:19: 9000000 INFO @ Thu, 08 Oct 2020 20:43:21: 22000000 INFO @ Thu, 08 Oct 2020 20:43:24: 16000000 INFO @ Thu, 08 Oct 2020 20:43:24: 10000000 INFO @ Thu, 08 Oct 2020 20:43:26: 23000000 INFO @ Thu, 08 Oct 2020 20:43:29: 17000000 INFO @ Thu, 08 Oct 2020 20:43:29: 11000000 INFO @ Thu, 08 Oct 2020 20:43:30: 24000000 INFO @ Thu, 08 Oct 2020 20:43:34: 18000000 INFO @ Thu, 08 Oct 2020 20:43:35: 12000000 INFO @ Thu, 08 Oct 2020 20:43:35: 25000000 INFO @ Thu, 08 Oct 2020 20:43:37: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:43:37: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:43:37: #1 total tags in treatment: 25355439 INFO @ Thu, 08 Oct 2020 20:43:37: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:43:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:43:38: #1 tags after filtering in treatment: 25355439 INFO @ Thu, 08 Oct 2020 20:43:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:43:38: #1 finished! INFO @ Thu, 08 Oct 2020 20:43:38: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:43:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:43:39: 19000000 INFO @ Thu, 08 Oct 2020 20:43:39: #2 number of paired peaks: 159 WARNING @ Thu, 08 Oct 2020 20:43:39: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Thu, 08 Oct 2020 20:43:39: start model_add_line... INFO @ Thu, 08 Oct 2020 20:43:39: start X-correlation... INFO @ Thu, 08 Oct 2020 20:43:39: end of X-cor INFO @ Thu, 08 Oct 2020 20:43:39: #2 finished! INFO @ Thu, 08 Oct 2020 20:43:39: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:43:39: #2 alternative fragment length(s) may be 1,36,41,112,594 bps INFO @ Thu, 08 Oct 2020 20:43:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05_model.r WARNING @ Thu, 08 Oct 2020 20:43:39: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:43:39: #2 You may need to consider one of the other alternative d(s): 1,36,41,112,594 WARNING @ Thu, 08 Oct 2020 20:43:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:43:39: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:43:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:43:40: 13000000 INFO @ Thu, 08 Oct 2020 20:43:44: 20000000 INFO @ Thu, 08 Oct 2020 20:43:45: 14000000 INFO @ Thu, 08 Oct 2020 20:43:49: 21000000 INFO @ Thu, 08 Oct 2020 20:43:50: 15000000 INFO @ Thu, 08 Oct 2020 20:43:54: 22000000 INFO @ Thu, 08 Oct 2020 20:43:55: 16000000 INFO @ Thu, 08 Oct 2020 20:43:59: 23000000 INFO @ Thu, 08 Oct 2020 20:44:00: 17000000 INFO @ Thu, 08 Oct 2020 20:44:04: 24000000 INFO @ Thu, 08 Oct 2020 20:44:05: 18000000 INFO @ Thu, 08 Oct 2020 20:44:09: 25000000 INFO @ Thu, 08 Oct 2020 20:44:10: 19000000 INFO @ Thu, 08 Oct 2020 20:44:11: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:44:11: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:44:11: #1 total tags in treatment: 25355439 INFO @ Thu, 08 Oct 2020 20:44:11: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:44:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:44:11: #1 tags after filtering in treatment: 25355439 INFO @ Thu, 08 Oct 2020 20:44:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:44:11: #1 finished! INFO @ Thu, 08 Oct 2020 20:44:11: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:44:13: #2 number of paired peaks: 159 WARNING @ Thu, 08 Oct 2020 20:44:13: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Thu, 08 Oct 2020 20:44:13: start model_add_line... INFO @ Thu, 08 Oct 2020 20:44:13: start X-correlation... INFO @ Thu, 08 Oct 2020 20:44:13: end of X-cor INFO @ Thu, 08 Oct 2020 20:44:13: #2 finished! INFO @ Thu, 08 Oct 2020 20:44:13: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:44:13: #2 alternative fragment length(s) may be 1,36,41,112,594 bps INFO @ Thu, 08 Oct 2020 20:44:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10_model.r WARNING @ Thu, 08 Oct 2020 20:44:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:44:13: #2 You may need to consider one of the other alternative d(s): 1,36,41,112,594 WARNING @ Thu, 08 Oct 2020 20:44:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:44:13: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:44:13: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:44:15: 20000000 INFO @ Thu, 08 Oct 2020 20:44:18: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:44:20: 21000000 INFO @ Thu, 08 Oct 2020 20:44:25: 22000000 INFO @ Thu, 08 Oct 2020 20:44:30: 23000000 INFO @ Thu, 08 Oct 2020 20:44:34: 24000000 INFO @ Thu, 08 Oct 2020 20:44:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:44:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:44:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05_summits.bed INFO @ Thu, 08 Oct 2020 20:44:35: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:44:39: 25000000 INFO @ Thu, 08 Oct 2020 20:44:41: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:44:41: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:44:41: #1 total tags in treatment: 25355439 INFO @ Thu, 08 Oct 2020 20:44:41: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:44:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:44:41: #1 tags after filtering in treatment: 25355439 INFO @ Thu, 08 Oct 2020 20:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:44:41: #1 finished! INFO @ Thu, 08 Oct 2020 20:44:41: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:44:43: #2 number of paired peaks: 159 WARNING @ Thu, 08 Oct 2020 20:44:43: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Thu, 08 Oct 2020 20:44:43: start model_add_line... INFO @ Thu, 08 Oct 2020 20:44:43: start X-correlation... INFO @ Thu, 08 Oct 2020 20:44:43: end of X-cor INFO @ Thu, 08 Oct 2020 20:44:43: #2 finished! INFO @ Thu, 08 Oct 2020 20:44:43: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:44:43: #2 alternative fragment length(s) may be 1,36,41,112,594 bps INFO @ Thu, 08 Oct 2020 20:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20_model.r WARNING @ Thu, 08 Oct 2020 20:44:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:44:43: #2 You may need to consider one of the other alternative d(s): 1,36,41,112,594 WARNING @ Thu, 08 Oct 2020 20:44:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:44:43: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:44:49: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:45:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:45:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:45:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10_summits.bed INFO @ Thu, 08 Oct 2020 20:45:07: 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 @ Thu, 08 Oct 2020 20:45:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:45:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:45:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:45:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20_summits.bed INFO @ Thu, 08 Oct 2020 20:45:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling