Job ID = 10165905 SRX = SRX6799187 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: 00:08:54 38150350 reads; of these: 38150350 (100.00%) were unpaired; of these: 1480865 (3.88%) aligned 0 times 29054037 (76.16%) aligned exactly 1 time 7615448 (19.96%) aligned >1 times 96.12% overall alignment rate Time searching: 00:08:54 Overall time: 00:08:54 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] 11562438 / 36669485 = 0.3153 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 20:24:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.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 20:24:18: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:24:18: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:24:23: 1000000 INFO @ Thu, 08 Oct 2020 20:24:28: 2000000 INFO @ Thu, 08 Oct 2020 20:24:33: 3000000 INFO @ Thu, 08 Oct 2020 20:24:38: 4000000 INFO @ Thu, 08 Oct 2020 20:24:43: 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 20:24:48: 6000000 INFO @ Thu, 08 Oct 2020 20:24:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.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 20:24:48: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:24:48: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:24:53: 7000000 INFO @ Thu, 08 Oct 2020 20:24:53: 1000000 INFO @ Thu, 08 Oct 2020 20:24:59: 8000000 INFO @ Thu, 08 Oct 2020 20:24:59: 2000000 INFO @ Thu, 08 Oct 2020 20:25:04: 9000000 INFO @ Thu, 08 Oct 2020 20:25:04: 3000000 INFO @ Thu, 08 Oct 2020 20:25:09: 10000000 INFO @ Thu, 08 Oct 2020 20:25:09: 4000000 INFO @ Thu, 08 Oct 2020 20:25:15: 5000000 INFO @ Thu, 08 Oct 2020 20:25:15: 11000000 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 20:25:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.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 20:25:18: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:25:18: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:25:21: 6000000 INFO @ Thu, 08 Oct 2020 20:25:21: 12000000 INFO @ Thu, 08 Oct 2020 20:25:24: 1000000 INFO @ Thu, 08 Oct 2020 20:25:26: 7000000 INFO @ Thu, 08 Oct 2020 20:25:26: 13000000 INFO @ Thu, 08 Oct 2020 20:25:29: 2000000 INFO @ Thu, 08 Oct 2020 20:25:32: 8000000 INFO @ Thu, 08 Oct 2020 20:25:32: 14000000 INFO @ Thu, 08 Oct 2020 20:25:35: 3000000 INFO @ Thu, 08 Oct 2020 20:25:37: 9000000 INFO @ Thu, 08 Oct 2020 20:25:38: 15000000 INFO @ Thu, 08 Oct 2020 20:25:41: 4000000 INFO @ Thu, 08 Oct 2020 20:25:43: 10000000 INFO @ Thu, 08 Oct 2020 20:25:44: 16000000 INFO @ Thu, 08 Oct 2020 20:25:47: 5000000 INFO @ Thu, 08 Oct 2020 20:25:49: 11000000 INFO @ Thu, 08 Oct 2020 20:25:50: 17000000 INFO @ Thu, 08 Oct 2020 20:25:53: 6000000 INFO @ Thu, 08 Oct 2020 20:25:55: 12000000 INFO @ Thu, 08 Oct 2020 20:25:56: 18000000 INFO @ Thu, 08 Oct 2020 20:25:58: 7000000 INFO @ Thu, 08 Oct 2020 20:26:01: 13000000 INFO @ Thu, 08 Oct 2020 20:26:03: 19000000 INFO @ Thu, 08 Oct 2020 20:26:05: 8000000 INFO @ Thu, 08 Oct 2020 20:26:07: 14000000 INFO @ Thu, 08 Oct 2020 20:26:09: 20000000 INFO @ Thu, 08 Oct 2020 20:26:11: 9000000 INFO @ Thu, 08 Oct 2020 20:26:13: 15000000 INFO @ Thu, 08 Oct 2020 20:26:15: 21000000 INFO @ Thu, 08 Oct 2020 20:26:16: 10000000 INFO @ Thu, 08 Oct 2020 20:26:20: 16000000 INFO @ Thu, 08 Oct 2020 20:26:21: 22000000 INFO @ Thu, 08 Oct 2020 20:26:22: 11000000 INFO @ Thu, 08 Oct 2020 20:26:26: 17000000 INFO @ Thu, 08 Oct 2020 20:26:27: 23000000 INFO @ Thu, 08 Oct 2020 20:26:28: 12000000 INFO @ Thu, 08 Oct 2020 20:26:32: 18000000 INFO @ Thu, 08 Oct 2020 20:26:34: 24000000 INFO @ Thu, 08 Oct 2020 20:26:34: 13000000 INFO @ Thu, 08 Oct 2020 20:26:38: 19000000 INFO @ Thu, 08 Oct 2020 20:26:40: 25000000 INFO @ Thu, 08 Oct 2020 20:26:40: 14000000 INFO @ Thu, 08 Oct 2020 20:26:40: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:26:40: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:26:40: #1 total tags in treatment: 25107047 INFO @ Thu, 08 Oct 2020 20:26:40: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:26:40: #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 20:26:41: #1 tags after filtering in treatment: 25107047 INFO @ Thu, 08 Oct 2020 20:26:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:26:41: #1 finished! INFO @ Thu, 08 Oct 2020 20:26:41: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:26:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:26:42: #2 number of paired peaks: 127 WARNING @ Thu, 08 Oct 2020 20:26:42: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Thu, 08 Oct 2020 20:26:42: start model_add_line... INFO @ Thu, 08 Oct 2020 20:26:43: start X-correlation... INFO @ Thu, 08 Oct 2020 20:26:43: end of X-cor INFO @ Thu, 08 Oct 2020 20:26:43: #2 finished! INFO @ Thu, 08 Oct 2020 20:26:43: #2 predicted fragment length is 138 bps INFO @ Thu, 08 Oct 2020 20:26:43: #2 alternative fragment length(s) may be 3,66,97,138 bps INFO @ Thu, 08 Oct 2020 20:26:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.05_model.r INFO @ Thu, 08 Oct 2020 20:26:43: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:26:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:26:44: 20000000 INFO @ Thu, 08 Oct 2020 20:26:47: 15000000 INFO @ Thu, 08 Oct 2020 20:26:50: 21000000 INFO @ Thu, 08 Oct 2020 20:26:53: 16000000 INFO @ Thu, 08 Oct 2020 20:26:56: 22000000 INFO @ Thu, 08 Oct 2020 20:26:59: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:27:02: 23000000 INFO @ Thu, 08 Oct 2020 20:27:05: 18000000 INFO @ Thu, 08 Oct 2020 20:27:08: 24000000 INFO @ Thu, 08 Oct 2020 20:27:11: 19000000 INFO @ Thu, 08 Oct 2020 20:27:14: 25000000 INFO @ Thu, 08 Oct 2020 20:27:15: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:27:15: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:27:15: #1 total tags in treatment: 25107047 INFO @ Thu, 08 Oct 2020 20:27:15: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:27:15: #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 20:27:16: #1 tags after filtering in treatment: 25107047 INFO @ Thu, 08 Oct 2020 20:27:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:27:16: #1 finished! INFO @ Thu, 08 Oct 2020 20:27:16: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:27:17: 20000000 INFO @ Thu, 08 Oct 2020 20:27:17: #2 number of paired peaks: 127 WARNING @ Thu, 08 Oct 2020 20:27:17: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Thu, 08 Oct 2020 20:27:17: start model_add_line... INFO @ Thu, 08 Oct 2020 20:27:17: start X-correlation... INFO @ Thu, 08 Oct 2020 20:27:17: end of X-cor INFO @ Thu, 08 Oct 2020 20:27:17: #2 finished! INFO @ Thu, 08 Oct 2020 20:27:17: #2 predicted fragment length is 138 bps INFO @ Thu, 08 Oct 2020 20:27:17: #2 alternative fragment length(s) may be 3,66,97,138 bps INFO @ Thu, 08 Oct 2020 20:27:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.10_model.r INFO @ Thu, 08 Oct 2020 20:27:17: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:27:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:27:23: 21000000 INFO @ Thu, 08 Oct 2020 20:27:29: 22000000 INFO @ Thu, 08 Oct 2020 20:27:31: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:27:35: 23000000 INFO @ Thu, 08 Oct 2020 20:27:41: 24000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:27:47: 25000000 INFO @ Thu, 08 Oct 2020 20:27:47: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:27:47: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:27:47: #1 total tags in treatment: 25107047 INFO @ Thu, 08 Oct 2020 20:27:47: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:27:47: #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 20:27:48: #1 tags after filtering in treatment: 25107047 INFO @ Thu, 08 Oct 2020 20:27:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:27:48: #1 finished! INFO @ Thu, 08 Oct 2020 20:27:48: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:27:49: #2 number of paired peaks: 127 WARNING @ Thu, 08 Oct 2020 20:27:49: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Thu, 08 Oct 2020 20:27:49: start model_add_line... INFO @ Thu, 08 Oct 2020 20:27:50: start X-correlation... INFO @ Thu, 08 Oct 2020 20:27:50: end of X-cor INFO @ Thu, 08 Oct 2020 20:27:50: #2 finished! INFO @ Thu, 08 Oct 2020 20:27:50: #2 predicted fragment length is 138 bps INFO @ Thu, 08 Oct 2020 20:27:50: #2 alternative fragment length(s) may be 3,66,97,138 bps INFO @ Thu, 08 Oct 2020 20:27:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.20_model.r INFO @ Thu, 08 Oct 2020 20:27:50: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:27:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:27:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:27:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:27:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.05_summits.bed INFO @ Thu, 08 Oct 2020 20:27:57: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (14457 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:28:05: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.10_summits.bed INFO @ Thu, 08 Oct 2020 20:28:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9220 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:28:38: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:29:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:29:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:29:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799187/SRX6799187.20_summits.bed INFO @ Thu, 08 Oct 2020 20:29:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3408 records, 4 fields): 4 millis CompletedMACS2peakCalling