Job ID = 6456720 SRX = SRX3981625 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:11:54 prefetch.2.10.7: 1) Downloading 'SRR7050259'... 2020-06-21T11:11:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:13:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:13:08 prefetch.2.10.7: 'SRR7050259' is valid 2020-06-21T11:13:08 prefetch.2.10.7: 1) 'SRR7050259' was downloaded successfully 2020-06-21T11:13:08 prefetch.2.10.7: 'SRR7050259' has 0 unresolved dependencies Read 12869402 spots for SRR7050259/SRR7050259.sra Written 12869402 spots for SRR7050259/SRR7050259.sra 2020-06-21T11:13:59 prefetch.2.10.7: 1) Downloading 'SRR7050260'... 2020-06-21T11:13:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:15:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:15:50 prefetch.2.10.7: 'SRR7050260' is valid 2020-06-21T11:15:50 prefetch.2.10.7: 1) 'SRR7050260' was downloaded successfully 2020-06-21T11:15:50 prefetch.2.10.7: 'SRR7050260' has 0 unresolved dependencies Read 12530390 spots for SRR7050260/SRR7050260.sra Written 12530390 spots for SRR7050260/SRR7050260.sra 2020-06-21T11:16:44 prefetch.2.10.7: 1) Downloading 'SRR7050261'... 2020-06-21T11:16:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:17:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:17:55 prefetch.2.10.7: 'SRR7050261' is valid 2020-06-21T11:17:55 prefetch.2.10.7: 1) 'SRR7050261' was downloaded successfully 2020-06-21T11:17:55 prefetch.2.10.7: 'SRR7050261' has 0 unresolved dependencies Read 12853850 spots for SRR7050261/SRR7050261.sra Written 12853850 spots for SRR7050261/SRR7050261.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: 00:10:16 38253642 reads; of these: 38253642 (100.00%) were unpaired; of these: 1202444 (3.14%) aligned 0 times 29430775 (76.94%) aligned exactly 1 time 7620423 (19.92%) aligned >1 times 96.86% overall alignment rate Time searching: 00:10:16 Overall time: 00:10:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 6097933 / 37051198 = 0.1646 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 @ Sun, 21 Jun 2020 20:38:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:38:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:16: 1000000 INFO @ Sun, 21 Jun 2020 20:38:22: 2000000 INFO @ Sun, 21 Jun 2020 20:38:28: 3000000 INFO @ Sun, 21 Jun 2020 20:38:33: 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 @ Sun, 21 Jun 2020 20:38:39: 5000000 INFO @ Sun, 21 Jun 2020 20:38:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:38:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:45: 6000000 INFO @ Sun, 21 Jun 2020 20:38:49: 1000000 INFO @ Sun, 21 Jun 2020 20:38:51: 7000000 INFO @ Sun, 21 Jun 2020 20:38:56: 2000000 INFO @ Sun, 21 Jun 2020 20:38:57: 8000000 INFO @ Sun, 21 Jun 2020 20:39:02: 3000000 INFO @ Sun, 21 Jun 2020 20:39:04: 9000000 INFO @ Sun, 21 Jun 2020 20:39:09: 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 @ Sun, 21 Jun 2020 20:39:10: 10000000 INFO @ Sun, 21 Jun 2020 20:39:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:39:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:16: 5000000 INFO @ Sun, 21 Jun 2020 20:39:17: 11000000 INFO @ Sun, 21 Jun 2020 20:39:18: 1000000 INFO @ Sun, 21 Jun 2020 20:39:23: 6000000 INFO @ Sun, 21 Jun 2020 20:39:24: 12000000 INFO @ Sun, 21 Jun 2020 20:39:26: 2000000 INFO @ Sun, 21 Jun 2020 20:39:30: 7000000 INFO @ Sun, 21 Jun 2020 20:39:31: 13000000 INFO @ Sun, 21 Jun 2020 20:39:34: 3000000 INFO @ Sun, 21 Jun 2020 20:39:37: 8000000 INFO @ Sun, 21 Jun 2020 20:39:38: 14000000 INFO @ Sun, 21 Jun 2020 20:39:41: 4000000 INFO @ Sun, 21 Jun 2020 20:39:44: 9000000 INFO @ Sun, 21 Jun 2020 20:39:44: 15000000 INFO @ Sun, 21 Jun 2020 20:39:49: 5000000 INFO @ Sun, 21 Jun 2020 20:39:51: 10000000 INFO @ Sun, 21 Jun 2020 20:39:51: 16000000 INFO @ Sun, 21 Jun 2020 20:39:57: 6000000 INFO @ Sun, 21 Jun 2020 20:39:58: 11000000 INFO @ Sun, 21 Jun 2020 20:39:58: 17000000 INFO @ Sun, 21 Jun 2020 20:40:04: 7000000 INFO @ Sun, 21 Jun 2020 20:40:05: 18000000 INFO @ Sun, 21 Jun 2020 20:40:05: 12000000 INFO @ Sun, 21 Jun 2020 20:40:11: 8000000 INFO @ Sun, 21 Jun 2020 20:40:12: 13000000 INFO @ Sun, 21 Jun 2020 20:40:12: 19000000 INFO @ Sun, 21 Jun 2020 20:40:19: 9000000 INFO @ Sun, 21 Jun 2020 20:40:19: 14000000 INFO @ Sun, 21 Jun 2020 20:40:19: 20000000 INFO @ Sun, 21 Jun 2020 20:40:26: 21000000 INFO @ Sun, 21 Jun 2020 20:40:26: 15000000 INFO @ Sun, 21 Jun 2020 20:40:26: 10000000 INFO @ Sun, 21 Jun 2020 20:40:33: 22000000 INFO @ Sun, 21 Jun 2020 20:40:34: 16000000 INFO @ Sun, 21 Jun 2020 20:40:34: 11000000 INFO @ Sun, 21 Jun 2020 20:40:40: 23000000 INFO @ Sun, 21 Jun 2020 20:40:40: 17000000 INFO @ Sun, 21 Jun 2020 20:40:41: 12000000 INFO @ Sun, 21 Jun 2020 20:40:47: 24000000 INFO @ Sun, 21 Jun 2020 20:40:48: 18000000 INFO @ Sun, 21 Jun 2020 20:40:49: 13000000 INFO @ Sun, 21 Jun 2020 20:40:55: 25000000 INFO @ Sun, 21 Jun 2020 20:40:55: 19000000 INFO @ Sun, 21 Jun 2020 20:40:56: 14000000 INFO @ Sun, 21 Jun 2020 20:41:02: 26000000 INFO @ Sun, 21 Jun 2020 20:41:03: 20000000 INFO @ Sun, 21 Jun 2020 20:41:04: 15000000 INFO @ Sun, 21 Jun 2020 20:41:10: 21000000 INFO @ Sun, 21 Jun 2020 20:41:10: 27000000 INFO @ Sun, 21 Jun 2020 20:41:11: 16000000 INFO @ Sun, 21 Jun 2020 20:41:17: 22000000 INFO @ Sun, 21 Jun 2020 20:41:17: 28000000 INFO @ Sun, 21 Jun 2020 20:41:19: 17000000 INFO @ Sun, 21 Jun 2020 20:41:24: 23000000 INFO @ Sun, 21 Jun 2020 20:41:25: 29000000 INFO @ Sun, 21 Jun 2020 20:41:26: 18000000 INFO @ Sun, 21 Jun 2020 20:41:32: 24000000 INFO @ Sun, 21 Jun 2020 20:41:32: 30000000 INFO @ Sun, 21 Jun 2020 20:41:34: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:41:39: 25000000 INFO @ Sun, 21 Jun 2020 20:41:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:41:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:41:39: #1 total tags in treatment: 30953265 INFO @ Sun, 21 Jun 2020 20:41:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:41:40: #1 tags after filtering in treatment: 30953210 INFO @ Sun, 21 Jun 2020 20:41:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:42: 20000000 INFO @ Sun, 21 Jun 2020 20:41:42: #2 number of paired peaks: 335 WARNING @ Sun, 21 Jun 2020 20:41:42: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 21 Jun 2020 20:41:42: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:42: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:42: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:42: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:42: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 20:41:42: #2 alternative fragment length(s) may be 3,97,113 bps INFO @ Sun, 21 Jun 2020 20:41:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.05_model.r INFO @ Sun, 21 Jun 2020 20:41:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:46: 26000000 INFO @ Sun, 21 Jun 2020 20:41:49: 21000000 INFO @ Sun, 21 Jun 2020 20:41:53: 27000000 INFO @ Sun, 21 Jun 2020 20:41:57: 22000000 INFO @ Sun, 21 Jun 2020 20:42:00: 28000000 INFO @ Sun, 21 Jun 2020 20:42:04: 23000000 INFO @ Sun, 21 Jun 2020 20:42:06: 29000000 INFO @ Sun, 21 Jun 2020 20:42:12: 24000000 INFO @ Sun, 21 Jun 2020 20:42:13: 30000000 INFO @ Sun, 21 Jun 2020 20:42:19: 25000000 INFO @ Sun, 21 Jun 2020 20:42:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:42:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:42:20: #1 total tags in treatment: 30953265 INFO @ Sun, 21 Jun 2020 20:42:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:42:20: #1 tags after filtering in treatment: 30953210 INFO @ Sun, 21 Jun 2020 20:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:20: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:22: #2 number of paired peaks: 335 WARNING @ Sun, 21 Jun 2020 20:42:22: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 21 Jun 2020 20:42:22: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:23: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:23: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:23: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:23: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 20:42:23: #2 alternative fragment length(s) may be 3,97,113 bps INFO @ Sun, 21 Jun 2020 20:42:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.10_model.r INFO @ Sun, 21 Jun 2020 20:42:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:26: 26000000 INFO @ Sun, 21 Jun 2020 20:42:34: 27000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:42:41: 28000000 INFO @ Sun, 21 Jun 2020 20:42:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:42:48: 29000000 INFO @ Sun, 21 Jun 2020 20:42:55: 30000000 INFO @ Sun, 21 Jun 2020 20:43:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:43:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:43:02: #1 total tags in treatment: 30953265 INFO @ Sun, 21 Jun 2020 20:43:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:43:03: #1 tags after filtering in treatment: 30953210 INFO @ Sun, 21 Jun 2020 20:43:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:03: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:05: #2 number of paired peaks: 335 WARNING @ Sun, 21 Jun 2020 20:43:05: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 21 Jun 2020 20:43:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:05: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 20:43:05: #2 alternative fragment length(s) may be 3,97,113 bps INFO @ Sun, 21 Jun 2020 20:43:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.20_model.r INFO @ Sun, 21 Jun 2020 20:43:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.05_summits.bed INFO @ Sun, 21 Jun 2020 20:43:15: Done! pass1 - making usageList (348 chroms): 2 millis pass2 - checking and writing primary data (9369 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:43:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.10_summits.bed INFO @ Sun, 21 Jun 2020 20:43:57: Done! pass1 - making usageList (207 chroms): 1 millis pass2 - checking and writing primary data (4802 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981625/SRX3981625.20_summits.bed INFO @ Sun, 21 Jun 2020 20:44:40: Done! pass1 - making usageList (135 chroms): 2 millis pass2 - checking and writing primary data (1363 records, 4 fields): 5 millis CompletedMACS2peakCalling