Job ID = 10166003 SRX = SRX8331160 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: 00:13:22 39676651 reads; of these: 39676651 (100.00%) were unpaired; of these: 165809 (0.42%) aligned 0 times 33489282 (84.41%) aligned exactly 1 time 6021560 (15.18%) aligned >1 times 99.58% overall alignment rate Time searching: 00:13:22 Overall time: 00:13:22 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 20 files... [bam_rmdupse_core] 15330277 / 39510842 = 0.3880 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 20:45:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.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 20:45:59: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:45:59: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:46:07: 1000000 INFO @ Thu, 08 Oct 2020 20:46:15: 2000000 INFO @ Thu, 08 Oct 2020 20:46:23: 3000000 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 20:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.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 20:46:29: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:46:29: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:46:32: 4000000 INFO @ Thu, 08 Oct 2020 20:46:38: 1000000 INFO @ Thu, 08 Oct 2020 20:46:41: 5000000 INFO @ Thu, 08 Oct 2020 20:46:47: 2000000 INFO @ Thu, 08 Oct 2020 20:46:51: 6000000 INFO @ Thu, 08 Oct 2020 20:46:56: 3000000 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 20:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.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 20:46:59: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:46:59: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:47:00: 7000000 INFO @ Thu, 08 Oct 2020 20:47:05: 4000000 INFO @ Thu, 08 Oct 2020 20:47:08: 1000000 INFO @ Thu, 08 Oct 2020 20:47:09: 8000000 INFO @ Thu, 08 Oct 2020 20:47:15: 5000000 INFO @ Thu, 08 Oct 2020 20:47:17: 2000000 INFO @ Thu, 08 Oct 2020 20:47:18: 9000000 INFO @ Thu, 08 Oct 2020 20:47:24: 6000000 INFO @ Thu, 08 Oct 2020 20:47:26: 3000000 INFO @ Thu, 08 Oct 2020 20:47:28: 10000000 INFO @ Thu, 08 Oct 2020 20:47:34: 7000000 INFO @ Thu, 08 Oct 2020 20:47:36: 4000000 INFO @ Thu, 08 Oct 2020 20:47:38: 11000000 INFO @ Thu, 08 Oct 2020 20:47:43: 8000000 INFO @ Thu, 08 Oct 2020 20:47:45: 5000000 INFO @ Thu, 08 Oct 2020 20:47:47: 12000000 INFO @ Thu, 08 Oct 2020 20:47:53: 9000000 INFO @ Thu, 08 Oct 2020 20:47:55: 6000000 INFO @ Thu, 08 Oct 2020 20:47:57: 13000000 INFO @ Thu, 08 Oct 2020 20:48:02: 10000000 INFO @ Thu, 08 Oct 2020 20:48:04: 7000000 INFO @ Thu, 08 Oct 2020 20:48:06: 14000000 INFO @ Thu, 08 Oct 2020 20:48:11: 11000000 INFO @ Thu, 08 Oct 2020 20:48:13: 8000000 INFO @ Thu, 08 Oct 2020 20:48:15: 15000000 INFO @ Thu, 08 Oct 2020 20:48:21: 12000000 INFO @ Thu, 08 Oct 2020 20:48:23: 9000000 INFO @ Thu, 08 Oct 2020 20:48:25: 16000000 INFO @ Thu, 08 Oct 2020 20:48:30: 13000000 INFO @ Thu, 08 Oct 2020 20:48:32: 10000000 INFO @ Thu, 08 Oct 2020 20:48:34: 17000000 INFO @ Thu, 08 Oct 2020 20:48:40: 14000000 INFO @ Thu, 08 Oct 2020 20:48:42: 11000000 INFO @ Thu, 08 Oct 2020 20:48:44: 18000000 INFO @ Thu, 08 Oct 2020 20:48:49: 15000000 INFO @ Thu, 08 Oct 2020 20:48:51: 12000000 INFO @ Thu, 08 Oct 2020 20:48:53: 19000000 INFO @ Thu, 08 Oct 2020 20:48:59: 16000000 INFO @ Thu, 08 Oct 2020 20:49:00: 13000000 INFO @ Thu, 08 Oct 2020 20:49:03: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:49:09: 17000000 INFO @ Thu, 08 Oct 2020 20:49:10: 14000000 INFO @ Thu, 08 Oct 2020 20:49:12: 21000000 INFO @ Thu, 08 Oct 2020 20:49:18: 18000000 INFO @ Thu, 08 Oct 2020 20:49:19: 15000000 INFO @ Thu, 08 Oct 2020 20:49:22: 22000000 INFO @ Thu, 08 Oct 2020 20:49:27: 19000000 INFO @ Thu, 08 Oct 2020 20:49:28: 16000000 INFO @ Thu, 08 Oct 2020 20:49:31: 23000000 INFO @ Thu, 08 Oct 2020 20:49:37: 20000000 INFO @ Thu, 08 Oct 2020 20:49:37: 17000000 INFO @ Thu, 08 Oct 2020 20:49:40: 24000000 INFO @ Thu, 08 Oct 2020 20:49:42: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 20:49:42: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 20:49:42: #1 total tags in treatment: 24180565 INFO @ Thu, 08 Oct 2020 20:49:42: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:49:42: #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 20:49:42: #1 tags after filtering in treatment: 24180565 INFO @ Thu, 08 Oct 2020 20:49:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:49:42: #1 finished! INFO @ Thu, 08 Oct 2020 20:49:42: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:49:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:49:44: #2 number of paired peaks: 135 WARNING @ Thu, 08 Oct 2020 20:49:44: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Thu, 08 Oct 2020 20:49:44: start model_add_line... INFO @ Thu, 08 Oct 2020 20:49:44: start X-correlation... INFO @ Thu, 08 Oct 2020 20:49:44: end of X-cor INFO @ Thu, 08 Oct 2020 20:49:44: #2 finished! INFO @ Thu, 08 Oct 2020 20:49:44: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:49:44: #2 alternative fragment length(s) may be 1,33,65,567,589 bps INFO @ Thu, 08 Oct 2020 20:49:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05_model.r WARNING @ Thu, 08 Oct 2020 20:49:44: #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 20:49:44: #2 You may need to consider one of the other alternative d(s): 1,33,65,567,589 WARNING @ Thu, 08 Oct 2020 20:49:44: #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 20:49:44: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:49:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:49:46: 18000000 INFO @ Thu, 08 Oct 2020 20:49:46: 21000000 INFO @ Thu, 08 Oct 2020 20:49:55: 19000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:49:55: 22000000 INFO @ Thu, 08 Oct 2020 20:50:04: 20000000 INFO @ Thu, 08 Oct 2020 20:50:05: 23000000 INFO @ Thu, 08 Oct 2020 20:50:14: 24000000 INFO @ Thu, 08 Oct 2020 20:50:14: 21000000 INFO @ Thu, 08 Oct 2020 20:50:15: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 20:50:15: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 20:50:15: #1 total tags in treatment: 24180565 INFO @ Thu, 08 Oct 2020 20:50:15: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:50:15: #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 20:50:16: #1 tags after filtering in treatment: 24180565 INFO @ Thu, 08 Oct 2020 20:50:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:50:16: #1 finished! INFO @ Thu, 08 Oct 2020 20:50:16: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:50:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:50:17: #2 number of paired peaks: 135 WARNING @ Thu, 08 Oct 2020 20:50:17: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Thu, 08 Oct 2020 20:50:17: start model_add_line... INFO @ Thu, 08 Oct 2020 20:50:17: start X-correlation... INFO @ Thu, 08 Oct 2020 20:50:17: end of X-cor INFO @ Thu, 08 Oct 2020 20:50:17: #2 finished! INFO @ Thu, 08 Oct 2020 20:50:17: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:50:17: #2 alternative fragment length(s) may be 1,33,65,567,589 bps INFO @ Thu, 08 Oct 2020 20:50:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10_model.r WARNING @ Thu, 08 Oct 2020 20:50:17: #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 20:50:17: #2 You may need to consider one of the other alternative d(s): 1,33,65,567,589 WARNING @ Thu, 08 Oct 2020 20:50:17: #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 20:50:17: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:50:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:50:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:50:22: 22000000 INFO @ Thu, 08 Oct 2020 20:50:31: 23000000 INFO @ Thu, 08 Oct 2020 20:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05_summits.bed INFO @ Thu, 08 Oct 2020 20:50:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:50:39: 24000000 INFO @ Thu, 08 Oct 2020 20:50:40: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 20:50:40: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 20:50:40: #1 total tags in treatment: 24180565 INFO @ Thu, 08 Oct 2020 20:50:40: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:50:40: #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 20:50:41: #1 tags after filtering in treatment: 24180565 INFO @ Thu, 08 Oct 2020 20:50:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:50:41: #1 finished! INFO @ Thu, 08 Oct 2020 20:50:41: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:50:42: #2 number of paired peaks: 135 WARNING @ Thu, 08 Oct 2020 20:50:42: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Thu, 08 Oct 2020 20:50:42: start model_add_line... INFO @ Thu, 08 Oct 2020 20:50:42: start X-correlation... INFO @ Thu, 08 Oct 2020 20:50:42: end of X-cor INFO @ Thu, 08 Oct 2020 20:50:42: #2 finished! INFO @ Thu, 08 Oct 2020 20:50:42: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:50:42: #2 alternative fragment length(s) may be 1,33,65,567,589 bps INFO @ Thu, 08 Oct 2020 20:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20_model.r WARNING @ Thu, 08 Oct 2020 20:50:42: #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 20:50:42: #2 You may need to consider one of the other alternative d(s): 1,33,65,567,589 WARNING @ Thu, 08 Oct 2020 20:50:42: #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 20:50:42: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:50:56: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10_summits.bed INFO @ Thu, 08 Oct 2020 20:51:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:51:18: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20_summits.bed INFO @ Thu, 08 Oct 2020 20:51:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling