Job ID = 6367034 SRX = SRX2737093 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:17:46 prefetch.2.10.7: 1) Downloading 'SRR5448131'... 2020-06-15T23:17:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:19:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:19:26 prefetch.2.10.7: 1) 'SRR5448131' was downloaded successfully 2020-06-15T23:19:26 prefetch.2.10.7: 'SRR5448131' has 0 unresolved dependencies Read 34691176 spots for SRR5448131/SRR5448131.sra Written 34691176 spots for SRR5448131/SRR5448131.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: 00:07:24 34691176 reads; of these: 34691176 (100.00%) were unpaired; of these: 2309291 (6.66%) aligned 0 times 28204235 (81.30%) aligned exactly 1 time 4177650 (12.04%) aligned >1 times 93.34% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 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] 10044138 / 32381885 = 0.3102 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 08:34:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.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 08:34:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:26: 1000000 INFO @ Tue, 16 Jun 2020 08:34:32: 2000000 INFO @ Tue, 16 Jun 2020 08:34:38: 3000000 INFO @ Tue, 16 Jun 2020 08:34:45: 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 08:34:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.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 08:34:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:51: 5000000 INFO @ Tue, 16 Jun 2020 08:34:56: 1000000 INFO @ Tue, 16 Jun 2020 08:34:58: 6000000 INFO @ Tue, 16 Jun 2020 08:35:02: 2000000 INFO @ Tue, 16 Jun 2020 08:35:05: 7000000 INFO @ Tue, 16 Jun 2020 08:35:08: 3000000 INFO @ Tue, 16 Jun 2020 08:35:12: 8000000 INFO @ Tue, 16 Jun 2020 08:35:14: 4000000 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 08:35:18: 9000000 INFO @ Tue, 16 Jun 2020 08:35:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.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 08:35:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:20: 5000000 INFO @ Tue, 16 Jun 2020 08:35:25: 10000000 INFO @ Tue, 16 Jun 2020 08:35:26: 1000000 INFO @ Tue, 16 Jun 2020 08:35:27: 6000000 INFO @ Tue, 16 Jun 2020 08:35:32: 11000000 INFO @ Tue, 16 Jun 2020 08:35:33: 7000000 INFO @ Tue, 16 Jun 2020 08:35:33: 2000000 INFO @ Tue, 16 Jun 2020 08:35:39: 12000000 INFO @ Tue, 16 Jun 2020 08:35:39: 8000000 INFO @ Tue, 16 Jun 2020 08:35:40: 3000000 INFO @ Tue, 16 Jun 2020 08:35:45: 9000000 INFO @ Tue, 16 Jun 2020 08:35:46: 13000000 INFO @ Tue, 16 Jun 2020 08:35:47: 4000000 INFO @ Tue, 16 Jun 2020 08:35:51: 10000000 INFO @ Tue, 16 Jun 2020 08:35:53: 14000000 INFO @ Tue, 16 Jun 2020 08:35:53: 5000000 INFO @ Tue, 16 Jun 2020 08:35:58: 11000000 INFO @ Tue, 16 Jun 2020 08:35:59: 15000000 INFO @ Tue, 16 Jun 2020 08:36:00: 6000000 INFO @ Tue, 16 Jun 2020 08:36:04: 12000000 INFO @ Tue, 16 Jun 2020 08:36:06: 16000000 INFO @ Tue, 16 Jun 2020 08:36:07: 7000000 INFO @ Tue, 16 Jun 2020 08:36:11: 13000000 INFO @ Tue, 16 Jun 2020 08:36:13: 17000000 INFO @ Tue, 16 Jun 2020 08:36:14: 8000000 INFO @ Tue, 16 Jun 2020 08:36:17: 14000000 INFO @ Tue, 16 Jun 2020 08:36:21: 18000000 INFO @ Tue, 16 Jun 2020 08:36:21: 9000000 INFO @ Tue, 16 Jun 2020 08:36:23: 15000000 INFO @ Tue, 16 Jun 2020 08:36:28: 19000000 INFO @ Tue, 16 Jun 2020 08:36:28: 10000000 INFO @ Tue, 16 Jun 2020 08:36:30: 16000000 INFO @ Tue, 16 Jun 2020 08:36:35: 11000000 INFO @ Tue, 16 Jun 2020 08:36:35: 20000000 INFO @ Tue, 16 Jun 2020 08:36:37: 17000000 INFO @ Tue, 16 Jun 2020 08:36:42: 12000000 INFO @ Tue, 16 Jun 2020 08:36:42: 21000000 INFO @ Tue, 16 Jun 2020 08:36:43: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:36:49: 13000000 INFO @ Tue, 16 Jun 2020 08:36:49: 22000000 INFO @ Tue, 16 Jun 2020 08:36:50: 19000000 INFO @ Tue, 16 Jun 2020 08:36:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:36:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:36:52: #1 total tags in treatment: 22337747 INFO @ Tue, 16 Jun 2020 08:36:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:52: #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 08:36:52: #1 tags after filtering in treatment: 22337747 INFO @ Tue, 16 Jun 2020 08:36:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:53: #2 number of paired peaks: 1424 INFO @ Tue, 16 Jun 2020 08:36:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:54: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 08:36:54: #2 alternative fragment length(s) may be 3,154,165 bps INFO @ Tue, 16 Jun 2020 08:36:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.05_model.r INFO @ Tue, 16 Jun 2020 08:36:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:56: 14000000 INFO @ Tue, 16 Jun 2020 08:36:57: 20000000 INFO @ Tue, 16 Jun 2020 08:37:03: 15000000 INFO @ Tue, 16 Jun 2020 08:37:03: 21000000 INFO @ Tue, 16 Jun 2020 08:37:10: 22000000 INFO @ Tue, 16 Jun 2020 08:37:10: 16000000 INFO @ Tue, 16 Jun 2020 08:37:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:37:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:37:12: #1 total tags in treatment: 22337747 INFO @ Tue, 16 Jun 2020 08:37:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:12: #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 08:37:12: #1 tags after filtering in treatment: 22337747 INFO @ Tue, 16 Jun 2020 08:37:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:14: #2 number of paired peaks: 1424 INFO @ Tue, 16 Jun 2020 08:37:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:14: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 08:37:14: #2 alternative fragment length(s) may be 3,154,165 bps INFO @ Tue, 16 Jun 2020 08:37:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.10_model.r INFO @ Tue, 16 Jun 2020 08:37:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:17: 17000000 INFO @ Tue, 16 Jun 2020 08:37:23: 18000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:30: 19000000 INFO @ Tue, 16 Jun 2020 08:37:36: 20000000 INFO @ Tue, 16 Jun 2020 08:37:43: 21000000 INFO @ Tue, 16 Jun 2020 08:37:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:49: 22000000 INFO @ Tue, 16 Jun 2020 08:37:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:37:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:37:51: #1 total tags in treatment: 22337747 INFO @ Tue, 16 Jun 2020 08:37:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:51: #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 08:37:52: #1 tags after filtering in treatment: 22337747 INFO @ Tue, 16 Jun 2020 08:37:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:53: #2 number of paired peaks: 1424 INFO @ Tue, 16 Jun 2020 08:37:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:53: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 08:37:53: #2 alternative fragment length(s) may be 3,154,165 bps INFO @ Tue, 16 Jun 2020 08:37:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.20_model.r INFO @ Tue, 16 Jun 2020 08:37:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:38:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.05_summits.bed INFO @ Tue, 16 Jun 2020 08:38:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (8309 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:38:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.10_summits.bed INFO @ Tue, 16 Jun 2020 08:38:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5217 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:38:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737093/SRX2737093.20_summits.bed INFO @ Tue, 16 Jun 2020 08:39:06: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2337 records, 4 fields): 3 millis CompletedMACS2peakCalling