Job ID = 10165904 SRX = SRX6799190 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: 00:07:56 34174635 reads; of these: 34174635 (100.00%) were unpaired; of these: 1372899 (4.02%) aligned 0 times 22952028 (67.16%) aligned exactly 1 time 9849708 (28.82%) aligned >1 times 95.98% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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 16 files... [bam_rmdupse_core] 10050986 / 32801736 = 0.3064 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 20:22:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.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 20:22:24: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:22:24: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:22:29: 1000000 INFO @ Thu, 08 Oct 2020 20:22:34: 2000000 INFO @ Thu, 08 Oct 2020 20:22:40: 3000000 INFO @ Thu, 08 Oct 2020 20:22:45: 4000000 INFO @ Thu, 08 Oct 2020 20:22:50: 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 @ Thu, 08 Oct 2020 20:22:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.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 20:22:54: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:22:54: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:22:55: 6000000 INFO @ Thu, 08 Oct 2020 20:22:59: 1000000 INFO @ Thu, 08 Oct 2020 20:23:00: 7000000 INFO @ Thu, 08 Oct 2020 20:23:04: 2000000 INFO @ Thu, 08 Oct 2020 20:23:05: 8000000 INFO @ Thu, 08 Oct 2020 20:23:10: 3000000 INFO @ Thu, 08 Oct 2020 20:23:11: 9000000 INFO @ Thu, 08 Oct 2020 20:23:15: 4000000 INFO @ Thu, 08 Oct 2020 20:23:16: 10000000 INFO @ Thu, 08 Oct 2020 20:23:20: 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 @ Thu, 08 Oct 2020 20:23:21: 11000000 INFO @ Thu, 08 Oct 2020 20:23:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.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 20:23:24: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:23:24: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:23:25: 6000000 INFO @ Thu, 08 Oct 2020 20:23:26: 12000000 INFO @ Thu, 08 Oct 2020 20:23:29: 1000000 INFO @ Thu, 08 Oct 2020 20:23:31: 7000000 INFO @ Thu, 08 Oct 2020 20:23:31: 13000000 INFO @ Thu, 08 Oct 2020 20:23:34: 2000000 INFO @ Thu, 08 Oct 2020 20:23:36: 8000000 INFO @ Thu, 08 Oct 2020 20:23:37: 14000000 INFO @ Thu, 08 Oct 2020 20:23:38: 3000000 INFO @ Thu, 08 Oct 2020 20:23:41: 9000000 INFO @ Thu, 08 Oct 2020 20:23:42: 15000000 INFO @ Thu, 08 Oct 2020 20:23:43: 4000000 INFO @ Thu, 08 Oct 2020 20:23:46: 10000000 INFO @ Thu, 08 Oct 2020 20:23:47: 16000000 INFO @ Thu, 08 Oct 2020 20:23:48: 5000000 INFO @ Thu, 08 Oct 2020 20:23:51: 11000000 INFO @ Thu, 08 Oct 2020 20:23:52: 17000000 INFO @ Thu, 08 Oct 2020 20:23:53: 6000000 INFO @ Thu, 08 Oct 2020 20:23:56: 12000000 INFO @ Thu, 08 Oct 2020 20:23:57: 18000000 INFO @ Thu, 08 Oct 2020 20:23:57: 7000000 INFO @ Thu, 08 Oct 2020 20:24:02: 13000000 INFO @ Thu, 08 Oct 2020 20:24:02: 8000000 INFO @ Thu, 08 Oct 2020 20:24:02: 19000000 INFO @ Thu, 08 Oct 2020 20:24:07: 14000000 INFO @ Thu, 08 Oct 2020 20:24:07: 9000000 INFO @ Thu, 08 Oct 2020 20:24:08: 20000000 INFO @ Thu, 08 Oct 2020 20:24:11: 10000000 INFO @ Thu, 08 Oct 2020 20:24:12: 15000000 INFO @ Thu, 08 Oct 2020 20:24:13: 21000000 INFO @ Thu, 08 Oct 2020 20:24:16: 11000000 INFO @ Thu, 08 Oct 2020 20:24:17: 16000000 INFO @ Thu, 08 Oct 2020 20:24:18: 22000000 INFO @ Thu, 08 Oct 2020 20:24:21: 12000000 INFO @ Thu, 08 Oct 2020 20:24:22: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:24:22: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:24:22: #1 total tags in treatment: 22750750 INFO @ Thu, 08 Oct 2020 20:24:22: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:24:22: #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 20:24:22: 17000000 INFO @ Thu, 08 Oct 2020 20:24:22: #1 tags after filtering in treatment: 22750750 INFO @ Thu, 08 Oct 2020 20:24:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:24:22: #1 finished! INFO @ Thu, 08 Oct 2020 20:24:22: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:24:24: #2 number of paired peaks: 402 WARNING @ Thu, 08 Oct 2020 20:24:24: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Thu, 08 Oct 2020 20:24:24: start model_add_line... INFO @ Thu, 08 Oct 2020 20:24:24: start X-correlation... INFO @ Thu, 08 Oct 2020 20:24:24: end of X-cor INFO @ Thu, 08 Oct 2020 20:24:24: #2 finished! INFO @ Thu, 08 Oct 2020 20:24:24: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 20:24:24: #2 alternative fragment length(s) may be 2,14 bps INFO @ Thu, 08 Oct 2020 20:24:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.05_model.r WARNING @ Thu, 08 Oct 2020 20:24:24: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:24:24: #2 You may need to consider one of the other alternative d(s): 2,14 WARNING @ Thu, 08 Oct 2020 20:24:24: #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 20:24:24: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:24:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:24:25: 13000000 INFO @ Thu, 08 Oct 2020 20:24:27: 18000000 INFO @ Thu, 08 Oct 2020 20:24:30: 14000000 INFO @ Thu, 08 Oct 2020 20:24:32: 19000000 INFO @ Thu, 08 Oct 2020 20:24:35: 15000000 INFO @ Thu, 08 Oct 2020 20:24:38: 20000000 INFO @ Thu, 08 Oct 2020 20:24:39: 16000000 INFO @ Thu, 08 Oct 2020 20:24:43: 21000000 INFO @ Thu, 08 Oct 2020 20:24:44: 17000000 INFO @ Thu, 08 Oct 2020 20:24:48: 22000000 INFO @ Thu, 08 Oct 2020 20:24:48: 18000000 INFO @ Thu, 08 Oct 2020 20:24:52: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:24:52: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:24:52: #1 total tags in treatment: 22750750 INFO @ Thu, 08 Oct 2020 20:24:52: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:24:52: #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 20:24:52: #1 tags after filtering in treatment: 22750750 INFO @ Thu, 08 Oct 2020 20:24:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:24:52: #1 finished! INFO @ Thu, 08 Oct 2020 20:24:52: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:24:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:24:53: 19000000 INFO @ Thu, 08 Oct 2020 20:24:54: #2 number of paired peaks: 402 WARNING @ Thu, 08 Oct 2020 20:24:54: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Thu, 08 Oct 2020 20:24:54: start model_add_line... INFO @ Thu, 08 Oct 2020 20:24:54: start X-correlation... INFO @ Thu, 08 Oct 2020 20:24:54: end of X-cor INFO @ Thu, 08 Oct 2020 20:24:54: #2 finished! INFO @ Thu, 08 Oct 2020 20:24:54: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 20:24:54: #2 alternative fragment length(s) may be 2,14 bps INFO @ Thu, 08 Oct 2020 20:24:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.10_model.r WARNING @ Thu, 08 Oct 2020 20:24:54: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:24:54: #2 You may need to consider one of the other alternative d(s): 2,14 WARNING @ Thu, 08 Oct 2020 20:24:54: #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 20:24:54: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:24:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:24:57: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:24:58: 20000000 INFO @ Thu, 08 Oct 2020 20:25:02: 21000000 INFO @ Thu, 08 Oct 2020 20:25:07: 22000000 INFO @ Thu, 08 Oct 2020 20:25:10: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:25:10: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:25:10: #1 total tags in treatment: 22750750 INFO @ Thu, 08 Oct 2020 20:25:10: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:25:10: #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 20:25:11: #1 tags after filtering in treatment: 22750750 INFO @ Thu, 08 Oct 2020 20:25:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:25:11: #1 finished! INFO @ Thu, 08 Oct 2020 20:25:11: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:25:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:25:12: #2 number of paired peaks: 402 WARNING @ Thu, 08 Oct 2020 20:25:12: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Thu, 08 Oct 2020 20:25:12: start model_add_line... INFO @ Thu, 08 Oct 2020 20:25:12: start X-correlation... INFO @ Thu, 08 Oct 2020 20:25:12: end of X-cor INFO @ Thu, 08 Oct 2020 20:25:12: #2 finished! INFO @ Thu, 08 Oct 2020 20:25:12: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 20:25:12: #2 alternative fragment length(s) may be 2,14 bps INFO @ Thu, 08 Oct 2020 20:25:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.20_model.r WARNING @ Thu, 08 Oct 2020 20:25:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:25:12: #2 You may need to consider one of the other alternative d(s): 2,14 WARNING @ Thu, 08 Oct 2020 20:25:12: #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 20:25:12: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:25:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:25:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:25:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:25:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.05_summits.bed INFO @ Thu, 08 Oct 2020 20:25:13: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:25:27: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:25:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:25:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:25:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.10_summits.bed INFO @ Thu, 08 Oct 2020 20:25:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:25:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:26:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:26:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:26:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799190/SRX6799190.20_summits.bed INFO @ Thu, 08 Oct 2020 20:26:03: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling