Job ID = 6366510 SRX = SRX1674090 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:58:38 prefetch.2.10.7: 1) Downloading 'SRR3320136'... 2020-06-15T22:58:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:35 prefetch.2.10.7: 1) 'SRR3320136' was downloaded successfully Read 50879695 spots for SRR3320136/SRR3320136.sra Written 50879695 spots for SRR3320136/SRR3320136.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: 00:11:14 50879695 reads; of these: 50879695 (100.00%) were unpaired; of these: 1506298 (2.96%) aligned 0 times 43371324 (85.24%) aligned exactly 1 time 6002073 (11.80%) aligned >1 times 97.04% overall alignment rate Time searching: 00:11:14 Overall time: 00:11:14 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 24 files... [bam_rmdupse_core] 21982350 / 49373397 = 0.4452 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 08:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.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 08:23:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:20: 1000000 INFO @ Tue, 16 Jun 2020 08:23:27: 2000000 INFO @ Tue, 16 Jun 2020 08:23:33: 3000000 INFO @ Tue, 16 Jun 2020 08:23:40: 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 08:23:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.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 08:23:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:46: 5000000 INFO @ Tue, 16 Jun 2020 08:23:50: 1000000 INFO @ Tue, 16 Jun 2020 08:23:53: 6000000 INFO @ Tue, 16 Jun 2020 08:23:57: 2000000 INFO @ Tue, 16 Jun 2020 08:23:59: 7000000 INFO @ Tue, 16 Jun 2020 08:24:03: 3000000 INFO @ Tue, 16 Jun 2020 08:24:06: 8000000 INFO @ Tue, 16 Jun 2020 08:24:10: 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 08:24:12: 9000000 INFO @ Tue, 16 Jun 2020 08:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.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 08:24:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:17: 5000000 INFO @ Tue, 16 Jun 2020 08:24:19: 10000000 INFO @ Tue, 16 Jun 2020 08:24:21: 1000000 INFO @ Tue, 16 Jun 2020 08:24:23: 6000000 INFO @ Tue, 16 Jun 2020 08:24:26: 11000000 INFO @ Tue, 16 Jun 2020 08:24:27: 2000000 INFO @ Tue, 16 Jun 2020 08:24:30: 7000000 INFO @ Tue, 16 Jun 2020 08:24:32: 12000000 INFO @ Tue, 16 Jun 2020 08:24:34: 3000000 INFO @ Tue, 16 Jun 2020 08:24:37: 8000000 INFO @ Tue, 16 Jun 2020 08:24:39: 13000000 INFO @ Tue, 16 Jun 2020 08:24:41: 4000000 INFO @ Tue, 16 Jun 2020 08:24:43: 9000000 INFO @ Tue, 16 Jun 2020 08:24:46: 14000000 INFO @ Tue, 16 Jun 2020 08:24:48: 5000000 INFO @ Tue, 16 Jun 2020 08:24:50: 10000000 INFO @ Tue, 16 Jun 2020 08:24:53: 15000000 INFO @ Tue, 16 Jun 2020 08:24:55: 6000000 INFO @ Tue, 16 Jun 2020 08:24:57: 11000000 INFO @ Tue, 16 Jun 2020 08:25:00: 16000000 INFO @ Tue, 16 Jun 2020 08:25:02: 7000000 INFO @ Tue, 16 Jun 2020 08:25:03: 12000000 INFO @ Tue, 16 Jun 2020 08:25:06: 17000000 INFO @ Tue, 16 Jun 2020 08:25:08: 8000000 INFO @ Tue, 16 Jun 2020 08:25:10: 13000000 INFO @ Tue, 16 Jun 2020 08:25:13: 18000000 INFO @ Tue, 16 Jun 2020 08:25:15: 9000000 INFO @ Tue, 16 Jun 2020 08:25:17: 14000000 INFO @ Tue, 16 Jun 2020 08:25:21: 19000000 INFO @ Tue, 16 Jun 2020 08:25:22: 10000000 INFO @ Tue, 16 Jun 2020 08:25:24: 15000000 INFO @ Tue, 16 Jun 2020 08:25:28: 20000000 INFO @ Tue, 16 Jun 2020 08:25:29: 11000000 INFO @ Tue, 16 Jun 2020 08:25:31: 16000000 INFO @ Tue, 16 Jun 2020 08:25:35: 21000000 INFO @ Tue, 16 Jun 2020 08:25:36: 12000000 INFO @ Tue, 16 Jun 2020 08:25:38: 17000000 INFO @ Tue, 16 Jun 2020 08:25:42: 22000000 INFO @ Tue, 16 Jun 2020 08:25:44: 13000000 INFO @ Tue, 16 Jun 2020 08:25:45: 18000000 INFO @ Tue, 16 Jun 2020 08:25:49: 23000000 INFO @ Tue, 16 Jun 2020 08:25:51: 14000000 INFO @ Tue, 16 Jun 2020 08:25:52: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:25:56: 24000000 INFO @ Tue, 16 Jun 2020 08:25:58: 15000000 INFO @ Tue, 16 Jun 2020 08:25:59: 20000000 INFO @ Tue, 16 Jun 2020 08:26:03: 25000000 INFO @ Tue, 16 Jun 2020 08:26:05: 16000000 INFO @ Tue, 16 Jun 2020 08:26:06: 21000000 INFO @ Tue, 16 Jun 2020 08:26:10: 26000000 INFO @ Tue, 16 Jun 2020 08:26:12: 17000000 INFO @ Tue, 16 Jun 2020 08:26:13: 22000000 INFO @ Tue, 16 Jun 2020 08:26:17: 27000000 INFO @ Tue, 16 Jun 2020 08:26:19: 18000000 INFO @ Tue, 16 Jun 2020 08:26:20: 23000000 INFO @ Tue, 16 Jun 2020 08:26:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:20: #1 total tags in treatment: 27391047 INFO @ Tue, 16 Jun 2020 08:26:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:20: #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 08:26:20: #1 tags after filtering in treatment: 27391047 INFO @ Tue, 16 Jun 2020 08:26:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:22: #2 number of paired peaks: 598 WARNING @ Tue, 16 Jun 2020 08:26:22: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:22: #2 predicted fragment length is 230 bps INFO @ Tue, 16 Jun 2020 08:26:22: #2 alternative fragment length(s) may be 2,201,230,260,290,323 bps INFO @ Tue, 16 Jun 2020 08:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.05_model.r INFO @ Tue, 16 Jun 2020 08:26:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:26: 19000000 INFO @ Tue, 16 Jun 2020 08:26:27: 24000000 INFO @ Tue, 16 Jun 2020 08:26:33: 25000000 INFO @ Tue, 16 Jun 2020 08:26:34: 20000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:26:40: 26000000 INFO @ Tue, 16 Jun 2020 08:26:41: 21000000 INFO @ Tue, 16 Jun 2020 08:26:47: 27000000 INFO @ Tue, 16 Jun 2020 08:26:48: 22000000 INFO @ Tue, 16 Jun 2020 08:26:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:49: #1 total tags in treatment: 27391047 INFO @ Tue, 16 Jun 2020 08:26:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:49: #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 08:26:50: #1 tags after filtering in treatment: 27391047 INFO @ Tue, 16 Jun 2020 08:26:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:52: #2 number of paired peaks: 598 WARNING @ Tue, 16 Jun 2020 08:26:52: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:52: #2 predicted fragment length is 230 bps INFO @ Tue, 16 Jun 2020 08:26:52: #2 alternative fragment length(s) may be 2,201,230,260,290,323 bps INFO @ Tue, 16 Jun 2020 08:26:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.10_model.r INFO @ Tue, 16 Jun 2020 08:26:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:55: 23000000 INFO @ Tue, 16 Jun 2020 08:27:01: 24000000 INFO @ Tue, 16 Jun 2020 08:27:08: 25000000 INFO @ Tue, 16 Jun 2020 08:27:14: 26000000 INFO @ Tue, 16 Jun 2020 08:27:21: 27000000 INFO @ Tue, 16 Jun 2020 08:27:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:27:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:27:23: #1 total tags in treatment: 27391047 INFO @ Tue, 16 Jun 2020 08:27:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:23: #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 08:27:24: #1 tags after filtering in treatment: 27391047 INFO @ Tue, 16 Jun 2020 08:27:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:26: #2 number of paired peaks: 598 WARNING @ Tue, 16 Jun 2020 08:27:26: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:26: #2 predicted fragment length is 230 bps INFO @ Tue, 16 Jun 2020 08:27:26: #2 alternative fragment length(s) may be 2,201,230,260,290,323 bps INFO @ Tue, 16 Jun 2020 08:27:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.20_model.r INFO @ Tue, 16 Jun 2020 08:27:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (10850 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7350 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674090/SRX1674090.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3800 records, 4 fields): 5 millis CompletedMACS2peakCalling