Job ID = 6507887 SRX = SRX494972 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:09:41 prefetch.2.10.7: 1) Downloading 'SRR1198504'... 2020-06-26T14:09:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:12:19 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:12:19 prefetch.2.10.7: 1) 'SRR1198504' was downloaded successfully Read 26851729 spots for SRR1198504/SRR1198504.sra Written 26851729 spots for SRR1198504/SRR1198504.sra 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: 00:05:41 26851729 reads; of these: 26851729 (100.00%) were unpaired; of these: 2408303 (8.97%) aligned 0 times 21065719 (78.45%) aligned exactly 1 time 3377707 (12.58%) aligned >1 times 91.03% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 16633371 / 24443426 = 0.6805 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 @ Fri, 26 Jun 2020 23:23:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.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 @ Fri, 26 Jun 2020 23:23:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:23:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:23:50: 1000000 INFO @ Fri, 26 Jun 2020 23:23:56: 2000000 INFO @ Fri, 26 Jun 2020 23:24:02: 3000000 INFO @ Fri, 26 Jun 2020 23:24:08: 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 @ Fri, 26 Jun 2020 23:24:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.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 @ Fri, 26 Jun 2020 23:24:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:24:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:24:14: 5000000 INFO @ Fri, 26 Jun 2020 23:24:19: 1000000 INFO @ Fri, 26 Jun 2020 23:24:21: 6000000 INFO @ Fri, 26 Jun 2020 23:24:24: 2000000 INFO @ Fri, 26 Jun 2020 23:24:27: 7000000 INFO @ Fri, 26 Jun 2020 23:24:29: 3000000 INFO @ Fri, 26 Jun 2020 23:24:32: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:24:32: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:24:32: #1 total tags in treatment: 7810055 INFO @ Fri, 26 Jun 2020 23:24:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:24:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:24:33: #1 tags after filtering in treatment: 7810055 INFO @ Fri, 26 Jun 2020 23:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:24:33: #1 finished! INFO @ Fri, 26 Jun 2020 23:24:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:24:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:24:33: #2 number of paired peaks: 3341 INFO @ Fri, 26 Jun 2020 23:24:33: start model_add_line... INFO @ Fri, 26 Jun 2020 23:24:33: start X-correlation... INFO @ Fri, 26 Jun 2020 23:24:33: end of X-cor INFO @ Fri, 26 Jun 2020 23:24:33: #2 finished! INFO @ Fri, 26 Jun 2020 23:24:33: #2 predicted fragment length is 118 bps INFO @ Fri, 26 Jun 2020 23:24:33: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 26 Jun 2020 23:24:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.05_model.r INFO @ Fri, 26 Jun 2020 23:24:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:24:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:24:34: 4000000 INFO @ Fri, 26 Jun 2020 23:24:39: 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 @ Fri, 26 Jun 2020 23:24:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.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 @ Fri, 26 Jun 2020 23:24:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:24:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:24:45: 6000000 INFO @ Fri, 26 Jun 2020 23:24:48: 1000000 INFO @ Fri, 26 Jun 2020 23:24:50: 7000000 INFO @ Fri, 26 Jun 2020 23:24:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:24:54: 2000000 INFO @ Fri, 26 Jun 2020 23:24:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:24:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:24:54: #1 total tags in treatment: 7810055 INFO @ Fri, 26 Jun 2020 23:24:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:24:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:24:54: #1 tags after filtering in treatment: 7810055 INFO @ Fri, 26 Jun 2020 23:24:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:24:54: #1 finished! INFO @ Fri, 26 Jun 2020 23:24:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:24:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:24:55: #2 number of paired peaks: 3341 INFO @ Fri, 26 Jun 2020 23:24:55: start model_add_line... INFO @ Fri, 26 Jun 2020 23:24:55: start X-correlation... INFO @ Fri, 26 Jun 2020 23:24:55: end of X-cor INFO @ Fri, 26 Jun 2020 23:24:55: #2 finished! INFO @ Fri, 26 Jun 2020 23:24:55: #2 predicted fragment length is 118 bps INFO @ Fri, 26 Jun 2020 23:24:55: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 26 Jun 2020 23:24:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.10_model.r INFO @ Fri, 26 Jun 2020 23:24:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:24:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:24:59: 3000000 INFO @ Fri, 26 Jun 2020 23:25:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:25:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:25:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.05_summits.bed INFO @ Fri, 26 Jun 2020 23:25:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6150 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:25:04: 4000000 INFO @ Fri, 26 Jun 2020 23:25:09: 5000000 INFO @ Fri, 26 Jun 2020 23:25:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:25:14: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:25:19: 7000000 INFO @ Fri, 26 Jun 2020 23:25:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.10_summits.bed INFO @ Fri, 26 Jun 2020 23:25:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4763 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:25:23: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:25:23: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:25:23: #1 total tags in treatment: 7810055 INFO @ Fri, 26 Jun 2020 23:25:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:25:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:25:23: #1 tags after filtering in treatment: 7810055 INFO @ Fri, 26 Jun 2020 23:25:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:25:23: #1 finished! INFO @ Fri, 26 Jun 2020 23:25:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:25:24: #2 number of paired peaks: 3341 INFO @ Fri, 26 Jun 2020 23:25:24: start model_add_line... INFO @ Fri, 26 Jun 2020 23:25:24: start X-correlation... INFO @ Fri, 26 Jun 2020 23:25:24: end of X-cor INFO @ Fri, 26 Jun 2020 23:25:24: #2 finished! INFO @ Fri, 26 Jun 2020 23:25:24: #2 predicted fragment length is 118 bps INFO @ Fri, 26 Jun 2020 23:25:24: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 26 Jun 2020 23:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.20_model.r INFO @ Fri, 26 Jun 2020 23:25:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:25:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:25:43: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:25:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:25:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:25:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494972/SRX494972.20_summits.bed INFO @ Fri, 26 Jun 2020 23:25:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3451 records, 4 fields): 5 millis CompletedMACS2peakCalling