Job ID = 6368990 SRX = SRX958295 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:41:57 prefetch.2.10.7: 1) Downloading 'SRR1917668'... 2020-06-16T00:41:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:49:06 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:49:06 prefetch.2.10.7: 1) 'SRR1917668' was downloaded successfully Read 34130372 spots for SRR1917668/SRR1917668.sra Written 34130372 spots for SRR1917668/SRR1917668.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: 00:08:22 34130372 reads; of these: 34130372 (100.00%) were unpaired; of these: 4879941 (14.30%) aligned 0 times 17279918 (50.63%) aligned exactly 1 time 11970513 (35.07%) aligned >1 times 85.70% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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 12 files... [bam_rmdupse_core] 20089815 / 29250431 = 0.6868 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 @ Tue, 16 Jun 2020 10:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.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 @ Tue, 16 Jun 2020 10:04:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:04:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:04:58: 1000000 INFO @ Tue, 16 Jun 2020 10:05:04: 2000000 INFO @ Tue, 16 Jun 2020 10:05:10: 3000000 INFO @ Tue, 16 Jun 2020 10:05:16: 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 @ Tue, 16 Jun 2020 10:05:22: 5000000 INFO @ Tue, 16 Jun 2020 10:05:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.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 @ Tue, 16 Jun 2020 10:05:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:05:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:05:28: 6000000 INFO @ Tue, 16 Jun 2020 10:05:29: 1000000 INFO @ Tue, 16 Jun 2020 10:05:34: 7000000 INFO @ Tue, 16 Jun 2020 10:05:35: 2000000 INFO @ Tue, 16 Jun 2020 10:05:40: 8000000 INFO @ Tue, 16 Jun 2020 10:05:42: 3000000 INFO @ Tue, 16 Jun 2020 10:05:47: 9000000 INFO @ Tue, 16 Jun 2020 10:05:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:05:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:05:48: #1 total tags in treatment: 9160616 INFO @ Tue, 16 Jun 2020 10:05:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:05:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:05:48: #1 tags after filtering in treatment: 9160616 INFO @ Tue, 16 Jun 2020 10:05:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:05:48: #1 finished! INFO @ Tue, 16 Jun 2020 10:05:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:05:49: 4000000 INFO @ Tue, 16 Jun 2020 10:05:49: #2 number of paired peaks: 4794 INFO @ Tue, 16 Jun 2020 10:05:49: start model_add_line... INFO @ Tue, 16 Jun 2020 10:05:49: start X-correlation... INFO @ Tue, 16 Jun 2020 10:05:49: end of X-cor INFO @ Tue, 16 Jun 2020 10:05:49: #2 finished! INFO @ Tue, 16 Jun 2020 10:05:49: #2 predicted fragment length is 228 bps INFO @ Tue, 16 Jun 2020 10:05:49: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 16 Jun 2020 10:05:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.05_model.r INFO @ Tue, 16 Jun 2020 10:05:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:05:49: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 10:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.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 @ Tue, 16 Jun 2020 10:05:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:05:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:05:56: 5000000 INFO @ Tue, 16 Jun 2020 10:05:59: 1000000 INFO @ Tue, 16 Jun 2020 10:06:02: 6000000 INFO @ Tue, 16 Jun 2020 10:06:05: 2000000 INFO @ Tue, 16 Jun 2020 10:06:09: 7000000 INFO @ Tue, 16 Jun 2020 10:06:12: 3000000 INFO @ Tue, 16 Jun 2020 10:06:16: 8000000 INFO @ Tue, 16 Jun 2020 10:06:18: 4000000 INFO @ Tue, 16 Jun 2020 10:06:23: 9000000 INFO @ Tue, 16 Jun 2020 10:06:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:06:24: 5000000 INFO @ Tue, 16 Jun 2020 10:06:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:06:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:06:24: #1 total tags in treatment: 9160616 INFO @ Tue, 16 Jun 2020 10:06:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:06:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:06:24: #1 tags after filtering in treatment: 9160616 INFO @ Tue, 16 Jun 2020 10:06:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:06:24: #1 finished! INFO @ Tue, 16 Jun 2020 10:06:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:06:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:06:25: #2 number of paired peaks: 4794 INFO @ Tue, 16 Jun 2020 10:06:25: start model_add_line... INFO @ Tue, 16 Jun 2020 10:06:25: start X-correlation... INFO @ Tue, 16 Jun 2020 10:06:26: end of X-cor INFO @ Tue, 16 Jun 2020 10:06:26: #2 finished! INFO @ Tue, 16 Jun 2020 10:06:26: #2 predicted fragment length is 228 bps INFO @ Tue, 16 Jun 2020 10:06:26: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 16 Jun 2020 10:06:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.10_model.r INFO @ Tue, 16 Jun 2020 10:06:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:06:30: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:06:36: 7000000 INFO @ Tue, 16 Jun 2020 10:06:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:06:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:06:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.05_summits.bed INFO @ Tue, 16 Jun 2020 10:06:37: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7470 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:06:42: 8000000 INFO @ Tue, 16 Jun 2020 10:06:48: 9000000 INFO @ Tue, 16 Jun 2020 10:06:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:06:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:06:49: #1 total tags in treatment: 9160616 INFO @ Tue, 16 Jun 2020 10:06:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:06:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:06:49: #1 tags after filtering in treatment: 9160616 INFO @ Tue, 16 Jun 2020 10:06:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:06:49: #1 finished! INFO @ Tue, 16 Jun 2020 10:06:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:06:50: #2 number of paired peaks: 4794 INFO @ Tue, 16 Jun 2020 10:06:50: start model_add_line... INFO @ Tue, 16 Jun 2020 10:06:50: start X-correlation... INFO @ Tue, 16 Jun 2020 10:06:50: end of X-cor INFO @ Tue, 16 Jun 2020 10:06:50: #2 finished! INFO @ Tue, 16 Jun 2020 10:06:50: #2 predicted fragment length is 228 bps INFO @ Tue, 16 Jun 2020 10:06:50: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 16 Jun 2020 10:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.20_model.r INFO @ Tue, 16 Jun 2020 10:06:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:06:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:07:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:07:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:07:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:07:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.10_summits.bed INFO @ Tue, 16 Jun 2020 10:07:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5684 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:07:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:07:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:07:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:07:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958295/SRX958295.20_summits.bed INFO @ Tue, 16 Jun 2020 10:07:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3783 records, 4 fields): 6 millis CompletedMACS2peakCalling