Job ID = 6368309 SRX = SRX494992 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:06:16 prefetch.2.10.7: 1) Downloading 'SRR1198524'... 2020-06-16T00:06:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:09:08 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:09:08 prefetch.2.10.7: 1) 'SRR1198524' was downloaded successfully Read 11863744 spots for SRR1198524/SRR1198524.sra Written 11863744 spots for SRR1198524/SRR1198524.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: 00:02:01 11863744 reads; of these: 11863744 (100.00%) were unpaired; of these: 1140236 (9.61%) aligned 0 times 9265553 (78.10%) aligned exactly 1 time 1457955 (12.29%) aligned >1 times 90.39% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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_rmdupse_core] 3202678 / 10723508 = 0.2987 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 09:14:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.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 09:14:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:32: 1000000 INFO @ Tue, 16 Jun 2020 09:14:37: 2000000 INFO @ Tue, 16 Jun 2020 09:14:42: 3000000 INFO @ Tue, 16 Jun 2020 09:14:47: 4000000 INFO @ Tue, 16 Jun 2020 09:14:52: 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 @ Tue, 16 Jun 2020 09:14:57: 6000000 INFO @ Tue, 16 Jun 2020 09:14:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.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 09:14:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:02: 7000000 INFO @ Tue, 16 Jun 2020 09:15:02: 1000000 INFO @ Tue, 16 Jun 2020 09:15:05: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:15:05: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:15:05: #1 total tags in treatment: 7520830 INFO @ Tue, 16 Jun 2020 09:15:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:05: #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 09:15:05: #1 tags after filtering in treatment: 7520830 INFO @ Tue, 16 Jun 2020 09:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:06: #2 number of paired peaks: 3869 INFO @ Tue, 16 Jun 2020 09:15:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:06: #2 predicted fragment length is 261 bps INFO @ Tue, 16 Jun 2020 09:15:06: #2 alternative fragment length(s) may be 261 bps INFO @ Tue, 16 Jun 2020 09:15:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.05_model.r INFO @ Tue, 16 Jun 2020 09:15:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:08: 2000000 INFO @ Tue, 16 Jun 2020 09:15:13: 3000000 INFO @ Tue, 16 Jun 2020 09:15:18: 4000000 INFO @ Tue, 16 Jun 2020 09:15:23: 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 @ Tue, 16 Jun 2020 09:15:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.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 09:15:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:28: 6000000 INFO @ Tue, 16 Jun 2020 09:15:33: 1000000 INFO @ Tue, 16 Jun 2020 09:15:33: 7000000 INFO @ Tue, 16 Jun 2020 09:15:36: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:15:36: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:15:36: #1 total tags in treatment: 7520830 INFO @ Tue, 16 Jun 2020 09:15:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:36: #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 09:15:36: #1 tags after filtering in treatment: 7520830 INFO @ Tue, 16 Jun 2020 09:15:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:37: #2 number of paired peaks: 3869 INFO @ Tue, 16 Jun 2020 09:15:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:37: #2 predicted fragment length is 261 bps INFO @ Tue, 16 Jun 2020 09:15:37: #2 alternative fragment length(s) may be 261 bps INFO @ Tue, 16 Jun 2020 09:15:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.10_model.r INFO @ Tue, 16 Jun 2020 09:15:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.05_summits.bed INFO @ Tue, 16 Jun 2020 09:15:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5122 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:38: 2000000 INFO @ Tue, 16 Jun 2020 09:15:43: 3000000 INFO @ Tue, 16 Jun 2020 09:15:48: 4000000 INFO @ Tue, 16 Jun 2020 09:15:53: 5000000 INFO @ Tue, 16 Jun 2020 09:15:58: 6000000 INFO @ Tue, 16 Jun 2020 09:15:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:03: 7000000 INFO @ Tue, 16 Jun 2020 09:16:06: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:16:06: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:16:06: #1 total tags in treatment: 7520830 INFO @ Tue, 16 Jun 2020 09:16:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:06: #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 09:16:06: #1 tags after filtering in treatment: 7520830 INFO @ Tue, 16 Jun 2020 09:16:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:06: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:16:07: #2 number of paired peaks: 3869 INFO @ Tue, 16 Jun 2020 09:16:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:07: #2 predicted fragment length is 261 bps INFO @ Tue, 16 Jun 2020 09:16:07: #2 alternative fragment length(s) may be 261 bps INFO @ Tue, 16 Jun 2020 09:16:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.20_model.r INFO @ Tue, 16 Jun 2020 09:16:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.10_summits.bed INFO @ Tue, 16 Jun 2020 09:16:08: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4221 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:16:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494992/SRX494992.20_summits.bed INFO @ Tue, 16 Jun 2020 09:16:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3356 records, 4 fields): 4 millis CompletedMACS2peakCalling