Job ID = 6507858 SRX = SRX494941 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T12:54:22 prefetch.2.10.7: 1) Downloading 'SRR1198473'... 2020-06-26T12:54:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:57:06 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:57:06 prefetch.2.10.7: 1) 'SRR1198473' was downloaded successfully Read 26509773 spots for SRR1198473/SRR1198473.sra Written 26509773 spots for SRR1198473/SRR1198473.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: 00:05:29 26509773 reads; of these: 26509773 (100.00%) were unpaired; of these: 1787541 (6.74%) aligned 0 times 21793187 (82.21%) aligned exactly 1 time 2929045 (11.05%) aligned >1 times 93.26% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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] 13330270 / 24722232 = 0.5392 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 22:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.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 22:09:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:09:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:09:53: 1000000 INFO @ Fri, 26 Jun 2020 22:09:58: 2000000 INFO @ Fri, 26 Jun 2020 22:10:03: 3000000 INFO @ Fri, 26 Jun 2020 22:10:08: 4000000 INFO @ Fri, 26 Jun 2020 22:10:14: 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 @ Fri, 26 Jun 2020 22:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.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 22:10:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:10:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:10:19: 6000000 INFO @ Fri, 26 Jun 2020 22:10:23: 1000000 INFO @ Fri, 26 Jun 2020 22:10:24: 7000000 INFO @ Fri, 26 Jun 2020 22:10:28: 2000000 INFO @ Fri, 26 Jun 2020 22:10:30: 8000000 INFO @ Fri, 26 Jun 2020 22:10:34: 3000000 INFO @ Fri, 26 Jun 2020 22:10:35: 9000000 INFO @ Fri, 26 Jun 2020 22:10:39: 4000000 INFO @ Fri, 26 Jun 2020 22:10:40: 10000000 INFO @ Fri, 26 Jun 2020 22:10:44: 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 22:10:46: 11000000 INFO @ Fri, 26 Jun 2020 22:10:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.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 22:10:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:10:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:10:48: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:10:48: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:10:48: #1 total tags in treatment: 11391962 INFO @ Fri, 26 Jun 2020 22:10:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:10:48: #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 22:10:48: #1 tags after filtering in treatment: 11391962 INFO @ Fri, 26 Jun 2020 22:10:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:10:48: #1 finished! INFO @ Fri, 26 Jun 2020 22:10:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:10:49: #2 number of paired peaks: 3377 INFO @ Fri, 26 Jun 2020 22:10:49: start model_add_line... INFO @ Fri, 26 Jun 2020 22:10:49: start X-correlation... INFO @ Fri, 26 Jun 2020 22:10:49: end of X-cor INFO @ Fri, 26 Jun 2020 22:10:49: #2 finished! INFO @ Fri, 26 Jun 2020 22:10:49: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 22:10:49: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 22:10:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.05_model.r INFO @ Fri, 26 Jun 2020 22:10:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:10:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:10:50: 6000000 INFO @ Fri, 26 Jun 2020 22:10:53: 1000000 INFO @ Fri, 26 Jun 2020 22:10:55: 7000000 INFO @ Fri, 26 Jun 2020 22:11:00: 2000000 INFO @ Fri, 26 Jun 2020 22:11:01: 8000000 INFO @ Fri, 26 Jun 2020 22:11:06: 3000000 INFO @ Fri, 26 Jun 2020 22:11:06: 9000000 INFO @ Fri, 26 Jun 2020 22:11:12: 4000000 INFO @ Fri, 26 Jun 2020 22:11:12: 10000000 INFO @ Fri, 26 Jun 2020 22:11:17: 11000000 INFO @ Fri, 26 Jun 2020 22:11:18: 5000000 INFO @ Fri, 26 Jun 2020 22:11:19: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:11:19: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:11:19: #1 total tags in treatment: 11391962 INFO @ Fri, 26 Jun 2020 22:11:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:11:19: #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 22:11:20: #1 tags after filtering in treatment: 11391962 INFO @ Fri, 26 Jun 2020 22:11:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:11:20: #1 finished! INFO @ Fri, 26 Jun 2020 22:11:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:11:21: #2 number of paired peaks: 3377 INFO @ Fri, 26 Jun 2020 22:11:21: start model_add_line... INFO @ Fri, 26 Jun 2020 22:11:21: start X-correlation... INFO @ Fri, 26 Jun 2020 22:11:21: end of X-cor INFO @ Fri, 26 Jun 2020 22:11:21: #2 finished! INFO @ Fri, 26 Jun 2020 22:11:21: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 22:11:21: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 22:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.10_model.r INFO @ Fri, 26 Jun 2020 22:11:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:11:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:11:24: 6000000 INFO @ Fri, 26 Jun 2020 22:11:29: 7000000 INFO @ Fri, 26 Jun 2020 22:11:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:11:35: 8000000 INFO @ Fri, 26 Jun 2020 22:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.05_summits.bed INFO @ Fri, 26 Jun 2020 22:11:36: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10537 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:11:41: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:11:47: 10000000 INFO @ Fri, 26 Jun 2020 22:11:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:11:53: 11000000 INFO @ Fri, 26 Jun 2020 22:11:55: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:11:55: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:11:55: #1 total tags in treatment: 11391962 INFO @ Fri, 26 Jun 2020 22:11:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:11:55: #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 22:11:55: #1 tags after filtering in treatment: 11391962 INFO @ Fri, 26 Jun 2020 22:11:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:11:55: #1 finished! INFO @ Fri, 26 Jun 2020 22:11:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:11:56: #2 number of paired peaks: 3377 INFO @ Fri, 26 Jun 2020 22:11:56: start model_add_line... INFO @ Fri, 26 Jun 2020 22:11:56: start X-correlation... INFO @ Fri, 26 Jun 2020 22:11:56: end of X-cor INFO @ Fri, 26 Jun 2020 22:11:56: #2 finished! INFO @ Fri, 26 Jun 2020 22:11:56: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 22:11:56: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 22:11:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.20_model.r INFO @ Fri, 26 Jun 2020 22:11:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:11:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:12:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.10_summits.bed INFO @ Fri, 26 Jun 2020 22:12:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7486 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:12:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:12:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:12:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:12:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494941/SRX494941.20_summits.bed INFO @ Fri, 26 Jun 2020 22:12:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4460 records, 4 fields): 5 millis CompletedMACS2peakCalling