Job ID = 6366541 SRX = SRX1769996 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:51:56 prefetch.2.10.7: 1) Downloading 'SRR3535776'... 2020-06-15T22:51:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:27 prefetch.2.10.7: 1) 'SRR3535776' was downloaded successfully Read 87175889 spots for SRR3535776/SRR3535776.sra Written 87175889 spots for SRR3535776/SRR3535776.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: 00:17:28 87175889 reads; of these: 87175889 (100.00%) were unpaired; of these: 11334648 (13.00%) aligned 0 times 62758618 (71.99%) aligned exactly 1 time 13082623 (15.01%) aligned >1 times 87.00% overall alignment rate Time searching: 00:17:28 Overall time: 00:17:28 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 32 files... [bam_rmdupse_core] 43526851 / 75841241 = 0.5739 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 08:36:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.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 08:36:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:19: 1000000 INFO @ Tue, 16 Jun 2020 08:36:25: 2000000 INFO @ Tue, 16 Jun 2020 08:36:31: 3000000 INFO @ Tue, 16 Jun 2020 08:36:36: 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 08:36:42: 5000000 INFO @ Tue, 16 Jun 2020 08:36:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.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 08:36:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:48: 6000000 INFO @ Tue, 16 Jun 2020 08:36:49: 1000000 INFO @ Tue, 16 Jun 2020 08:36:54: 7000000 INFO @ Tue, 16 Jun 2020 08:36:55: 2000000 INFO @ Tue, 16 Jun 2020 08:37:00: 8000000 INFO @ Tue, 16 Jun 2020 08:37:01: 3000000 INFO @ Tue, 16 Jun 2020 08:37:06: 9000000 INFO @ Tue, 16 Jun 2020 08:37:07: 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 08:37:12: 10000000 INFO @ Tue, 16 Jun 2020 08:37:13: 5000000 INFO @ Tue, 16 Jun 2020 08:37:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.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 08:37:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:18: 11000000 INFO @ Tue, 16 Jun 2020 08:37:19: 1000000 INFO @ Tue, 16 Jun 2020 08:37:19: 6000000 INFO @ Tue, 16 Jun 2020 08:37:24: 2000000 INFO @ Tue, 16 Jun 2020 08:37:24: 12000000 INFO @ Tue, 16 Jun 2020 08:37:25: 7000000 INFO @ Tue, 16 Jun 2020 08:37:29: 3000000 INFO @ Tue, 16 Jun 2020 08:37:31: 13000000 INFO @ Tue, 16 Jun 2020 08:37:31: 8000000 INFO @ Tue, 16 Jun 2020 08:37:35: 4000000 INFO @ Tue, 16 Jun 2020 08:37:37: 14000000 INFO @ Tue, 16 Jun 2020 08:37:37: 9000000 INFO @ Tue, 16 Jun 2020 08:37:40: 5000000 INFO @ Tue, 16 Jun 2020 08:37:43: 15000000 INFO @ Tue, 16 Jun 2020 08:37:43: 10000000 INFO @ Tue, 16 Jun 2020 08:37:46: 6000000 INFO @ Tue, 16 Jun 2020 08:37:49: 16000000 INFO @ Tue, 16 Jun 2020 08:37:49: 11000000 INFO @ Tue, 16 Jun 2020 08:37:51: 7000000 INFO @ Tue, 16 Jun 2020 08:37:55: 17000000 INFO @ Tue, 16 Jun 2020 08:37:56: 12000000 INFO @ Tue, 16 Jun 2020 08:37:56: 8000000 INFO @ Tue, 16 Jun 2020 08:38:01: 18000000 INFO @ Tue, 16 Jun 2020 08:38:02: 13000000 INFO @ Tue, 16 Jun 2020 08:38:02: 9000000 INFO @ Tue, 16 Jun 2020 08:38:07: 10000000 INFO @ Tue, 16 Jun 2020 08:38:08: 19000000 INFO @ Tue, 16 Jun 2020 08:38:08: 14000000 INFO @ Tue, 16 Jun 2020 08:38:13: 11000000 INFO @ Tue, 16 Jun 2020 08:38:14: 20000000 INFO @ Tue, 16 Jun 2020 08:38:14: 15000000 INFO @ Tue, 16 Jun 2020 08:38:18: 12000000 INFO @ Tue, 16 Jun 2020 08:38:20: 21000000 INFO @ Tue, 16 Jun 2020 08:38:20: 16000000 INFO @ Tue, 16 Jun 2020 08:38:23: 13000000 INFO @ Tue, 16 Jun 2020 08:38:26: 22000000 INFO @ Tue, 16 Jun 2020 08:38:26: 17000000 INFO @ Tue, 16 Jun 2020 08:38:29: 14000000 INFO @ Tue, 16 Jun 2020 08:38:32: 23000000 INFO @ Tue, 16 Jun 2020 08:38:32: 18000000 INFO @ Tue, 16 Jun 2020 08:38:34: 15000000 INFO @ Tue, 16 Jun 2020 08:38:38: 24000000 INFO @ Tue, 16 Jun 2020 08:38:38: 19000000 INFO @ Tue, 16 Jun 2020 08:38:40: 16000000 INFO @ Tue, 16 Jun 2020 08:38:44: 20000000 INFO @ Tue, 16 Jun 2020 08:38:44: 25000000 INFO @ Tue, 16 Jun 2020 08:38:45: 17000000 INFO @ Tue, 16 Jun 2020 08:38:50: 18000000 INFO @ Tue, 16 Jun 2020 08:38:50: 21000000 INFO @ Tue, 16 Jun 2020 08:38:50: 26000000 INFO @ Tue, 16 Jun 2020 08:38:55: 19000000 INFO @ Tue, 16 Jun 2020 08:38:56: 22000000 INFO @ Tue, 16 Jun 2020 08:38:56: 27000000 INFO @ Tue, 16 Jun 2020 08:39:01: 20000000 INFO @ Tue, 16 Jun 2020 08:39:02: 23000000 INFO @ Tue, 16 Jun 2020 08:39:03: 28000000 INFO @ Tue, 16 Jun 2020 08:39:06: 21000000 INFO @ Tue, 16 Jun 2020 08:39:08: 24000000 INFO @ Tue, 16 Jun 2020 08:39:09: 29000000 INFO @ Tue, 16 Jun 2020 08:39:11: 22000000 INFO @ Tue, 16 Jun 2020 08:39:14: 25000000 INFO @ Tue, 16 Jun 2020 08:39:15: 30000000 INFO @ Tue, 16 Jun 2020 08:39:17: 23000000 INFO @ Tue, 16 Jun 2020 08:39:20: 26000000 INFO @ Tue, 16 Jun 2020 08:39:21: 31000000 INFO @ Tue, 16 Jun 2020 08:39:22: 24000000 INFO @ Tue, 16 Jun 2020 08:39:26: 27000000 INFO @ Tue, 16 Jun 2020 08:39:27: 32000000 INFO @ Tue, 16 Jun 2020 08:39:27: 25000000 INFO @ Tue, 16 Jun 2020 08:39:29: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:39:29: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:39:29: #1 total tags in treatment: 32314390 INFO @ Tue, 16 Jun 2020 08:39:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:29: #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 08:39:29: #1 tags after filtering in treatment: 32314390 INFO @ Tue, 16 Jun 2020 08:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:31: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 08:39:31: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:32: #2 predicted fragment length is 235 bps INFO @ Tue, 16 Jun 2020 08:39:32: #2 alternative fragment length(s) may be 1,140,193,214,235,248,269,296,312,348,470,488,527 bps INFO @ Tue, 16 Jun 2020 08:39:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.05_model.r INFO @ Tue, 16 Jun 2020 08:39:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:32: 28000000 INFO @ Tue, 16 Jun 2020 08:39:32: 26000000 INFO @ Tue, 16 Jun 2020 08:39:38: 27000000 INFO @ Tue, 16 Jun 2020 08:39:39: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:39:43: 28000000 INFO @ Tue, 16 Jun 2020 08:39:45: 30000000 INFO @ Tue, 16 Jun 2020 08:39:48: 29000000 INFO @ Tue, 16 Jun 2020 08:39:51: 31000000 INFO @ Tue, 16 Jun 2020 08:39:53: 30000000 INFO @ Tue, 16 Jun 2020 08:39:57: 32000000 INFO @ Tue, 16 Jun 2020 08:39:59: 31000000 INFO @ Tue, 16 Jun 2020 08:39:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:39:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:39:59: #1 total tags in treatment: 32314390 INFO @ Tue, 16 Jun 2020 08:39:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:59: #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 08:39:59: #1 tags after filtering in treatment: 32314390 INFO @ Tue, 16 Jun 2020 08:39:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:01: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 08:40:01: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:02: #2 predicted fragment length is 235 bps INFO @ Tue, 16 Jun 2020 08:40:02: #2 alternative fragment length(s) may be 1,140,193,214,235,248,269,296,312,348,470,488,527 bps INFO @ Tue, 16 Jun 2020 08:40:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.10_model.r INFO @ Tue, 16 Jun 2020 08:40:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:04: 32000000 INFO @ Tue, 16 Jun 2020 08:40:06: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:40:06: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:40:06: #1 total tags in treatment: 32314390 INFO @ Tue, 16 Jun 2020 08:40:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:06: #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 08:40:06: #1 tags after filtering in treatment: 32314390 INFO @ Tue, 16 Jun 2020 08:40:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:08: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 08:40:08: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:09: #2 predicted fragment length is 235 bps INFO @ Tue, 16 Jun 2020 08:40:09: #2 alternative fragment length(s) may be 1,140,193,214,235,248,269,296,312,348,470,488,527 bps INFO @ Tue, 16 Jun 2020 08:40:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.20_model.r INFO @ Tue, 16 Jun 2020 08:40:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:40:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.05_summits.bed INFO @ Tue, 16 Jun 2020 08:41:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (8282 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.10_summits.bed INFO @ Tue, 16 Jun 2020 08:41:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6036 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769996/SRX1769996.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4028 records, 4 fields): 5 millis CompletedMACS2peakCalling