Job ID = 6456724 SRX = SRX3981628 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:03:46 prefetch.2.10.7: 1) Downloading 'SRR7050268'... 2020-06-21T11:03:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:04:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:04:48 prefetch.2.10.7: 'SRR7050268' is valid 2020-06-21T11:04:48 prefetch.2.10.7: 1) 'SRR7050268' was downloaded successfully 2020-06-21T11:04:48 prefetch.2.10.7: 'SRR7050268' has 0 unresolved dependencies Read 11924903 spots for SRR7050268/SRR7050268.sra Written 11924903 spots for SRR7050268/SRR7050268.sra 2020-06-21T11:05:35 prefetch.2.10.7: 1) Downloading 'SRR7050269'... 2020-06-21T11:05:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:06:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:06:19 prefetch.2.10.7: 'SRR7050269' is valid 2020-06-21T11:06:19 prefetch.2.10.7: 1) 'SRR7050269' was downloaded successfully 2020-06-21T11:06:19 prefetch.2.10.7: 'SRR7050269' has 0 unresolved dependencies Read 11794131 spots for SRR7050269/SRR7050269.sra Written 11794131 spots for SRR7050269/SRR7050269.sra 2020-06-21T11:07:04 prefetch.2.10.7: 1) Downloading 'SRR7050270'... 2020-06-21T11:07:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:08:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:08:33 prefetch.2.10.7: 'SRR7050270' is valid 2020-06-21T11:08:33 prefetch.2.10.7: 1) 'SRR7050270' was downloaded successfully 2020-06-21T11:08:33 prefetch.2.10.7: 'SRR7050270' has 0 unresolved dependencies Read 11918519 spots for SRR7050270/SRR7050270.sra Written 11918519 spots for SRR7050270/SRR7050270.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: 00:08:26 35637553 reads; of these: 35637553 (100.00%) were unpaired; of these: 978241 (2.74%) aligned 0 times 28102428 (78.86%) aligned exactly 1 time 6556884 (18.40%) aligned >1 times 97.26% overall alignment rate Time searching: 00:08:26 Overall time: 00:08:26 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] 6051334 / 34659312 = 0.1746 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 20:25:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.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 20:25:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:43: 1000000 INFO @ Sun, 21 Jun 2020 20:25:48: 2000000 INFO @ Sun, 21 Jun 2020 20:25:53: 3000000 INFO @ Sun, 21 Jun 2020 20:25:58: 4000000 INFO @ Sun, 21 Jun 2020 20:26:03: 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 @ Sun, 21 Jun 2020 20:26:08: 6000000 INFO @ Sun, 21 Jun 2020 20:26:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.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 20:26:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:13: 7000000 INFO @ Sun, 21 Jun 2020 20:26:15: 1000000 INFO @ Sun, 21 Jun 2020 20:26:18: 8000000 INFO @ Sun, 21 Jun 2020 20:26:21: 2000000 INFO @ Sun, 21 Jun 2020 20:26:23: 9000000 INFO @ Sun, 21 Jun 2020 20:26:27: 3000000 INFO @ Sun, 21 Jun 2020 20:26:29: 10000000 INFO @ Sun, 21 Jun 2020 20:26:32: 4000000 INFO @ Sun, 21 Jun 2020 20:26:34: 11000000 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 20:26:38: 5000000 INFO @ Sun, 21 Jun 2020 20:26:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.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 20:26:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:39: 12000000 INFO @ Sun, 21 Jun 2020 20:26:44: 1000000 INFO @ Sun, 21 Jun 2020 20:26:44: 6000000 INFO @ Sun, 21 Jun 2020 20:26:45: 13000000 INFO @ Sun, 21 Jun 2020 20:26:49: 2000000 INFO @ Sun, 21 Jun 2020 20:26:50: 7000000 INFO @ Sun, 21 Jun 2020 20:26:50: 14000000 INFO @ Sun, 21 Jun 2020 20:26:55: 3000000 INFO @ Sun, 21 Jun 2020 20:26:56: 15000000 INFO @ Sun, 21 Jun 2020 20:26:56: 8000000 INFO @ Sun, 21 Jun 2020 20:27:00: 4000000 INFO @ Sun, 21 Jun 2020 20:27:01: 16000000 INFO @ Sun, 21 Jun 2020 20:27:02: 9000000 INFO @ Sun, 21 Jun 2020 20:27:05: 5000000 INFO @ Sun, 21 Jun 2020 20:27:07: 17000000 INFO @ Sun, 21 Jun 2020 20:27:08: 10000000 INFO @ Sun, 21 Jun 2020 20:27:11: 6000000 INFO @ Sun, 21 Jun 2020 20:27:12: 18000000 INFO @ Sun, 21 Jun 2020 20:27:14: 11000000 INFO @ Sun, 21 Jun 2020 20:27:16: 7000000 INFO @ Sun, 21 Jun 2020 20:27:18: 19000000 INFO @ Sun, 21 Jun 2020 20:27:20: 12000000 INFO @ Sun, 21 Jun 2020 20:27:21: 8000000 INFO @ Sun, 21 Jun 2020 20:27:23: 20000000 INFO @ Sun, 21 Jun 2020 20:27:26: 13000000 INFO @ Sun, 21 Jun 2020 20:27:27: 9000000 INFO @ Sun, 21 Jun 2020 20:27:28: 21000000 INFO @ Sun, 21 Jun 2020 20:27:32: 10000000 INFO @ Sun, 21 Jun 2020 20:27:32: 14000000 INFO @ Sun, 21 Jun 2020 20:27:34: 22000000 INFO @ Sun, 21 Jun 2020 20:27:37: 11000000 INFO @ Sun, 21 Jun 2020 20:27:38: 15000000 INFO @ Sun, 21 Jun 2020 20:27:39: 23000000 INFO @ Sun, 21 Jun 2020 20:27:43: 12000000 INFO @ Sun, 21 Jun 2020 20:27:44: 16000000 INFO @ Sun, 21 Jun 2020 20:27:45: 24000000 INFO @ Sun, 21 Jun 2020 20:27:48: 13000000 INFO @ Sun, 21 Jun 2020 20:27:51: 17000000 INFO @ Sun, 21 Jun 2020 20:27:51: 25000000 INFO @ Sun, 21 Jun 2020 20:27:54: 14000000 INFO @ Sun, 21 Jun 2020 20:27:56: 26000000 INFO @ Sun, 21 Jun 2020 20:27:57: 18000000 INFO @ Sun, 21 Jun 2020 20:28:00: 15000000 INFO @ Sun, 21 Jun 2020 20:28:02: 27000000 INFO @ Sun, 21 Jun 2020 20:28:03: 19000000 INFO @ Sun, 21 Jun 2020 20:28:05: 16000000 INFO @ Sun, 21 Jun 2020 20:28:07: 28000000 INFO @ Sun, 21 Jun 2020 20:28:09: 20000000 INFO @ Sun, 21 Jun 2020 20:28:11: 17000000 INFO @ Sun, 21 Jun 2020 20:28:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:28:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:28:11: #1 total tags in treatment: 28607978 INFO @ Sun, 21 Jun 2020 20:28:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:11: #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 20:28:12: #1 tags after filtering in treatment: 28607911 INFO @ Sun, 21 Jun 2020 20:28:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:12: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:14: #2 number of paired peaks: 702 WARNING @ Sun, 21 Jun 2020 20:28:14: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sun, 21 Jun 2020 20:28:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:14: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 20:28:14: #2 alternative fragment length(s) may be 4,138 bps INFO @ Sun, 21 Jun 2020 20:28:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.05_model.r INFO @ Sun, 21 Jun 2020 20:28:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:28:16: 21000000 INFO @ Sun, 21 Jun 2020 20:28:16: 18000000 INFO @ Sun, 21 Jun 2020 20:28:22: 22000000 INFO @ Sun, 21 Jun 2020 20:28:22: 19000000 INFO @ Sun, 21 Jun 2020 20:28:28: 20000000 INFO @ Sun, 21 Jun 2020 20:28:28: 23000000 INFO @ Sun, 21 Jun 2020 20:28:33: 21000000 INFO @ Sun, 21 Jun 2020 20:28:34: 24000000 INFO @ Sun, 21 Jun 2020 20:28:39: 22000000 INFO @ Sun, 21 Jun 2020 20:28:41: 25000000 INFO @ Sun, 21 Jun 2020 20:28:45: 23000000 INFO @ Sun, 21 Jun 2020 20:28:48: 26000000 INFO @ Sun, 21 Jun 2020 20:28:51: 24000000 INFO @ Sun, 21 Jun 2020 20:28:54: 27000000 INFO @ Sun, 21 Jun 2020 20:28:57: 25000000 INFO @ Sun, 21 Jun 2020 20:29:00: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:29:03: 26000000 INFO @ Sun, 21 Jun 2020 20:29:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:04: #1 total tags in treatment: 28607978 INFO @ Sun, 21 Jun 2020 20:29:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:04: #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 20:29:05: #1 tags after filtering in treatment: 28607911 INFO @ Sun, 21 Jun 2020 20:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:07: #2 number of paired peaks: 702 WARNING @ Sun, 21 Jun 2020 20:29:07: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:08: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 20:29:08: #2 alternative fragment length(s) may be 4,138 bps INFO @ Sun, 21 Jun 2020 20:29:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.10_model.r INFO @ Sun, 21 Jun 2020 20:29:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:08: 27000000 INFO @ Sun, 21 Jun 2020 20:29:14: 28000000 INFO @ Sun, 21 Jun 2020 20:29:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:18: #1 total tags in treatment: 28607978 INFO @ Sun, 21 Jun 2020 20:29:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:18: #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 20:29:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:18: #1 tags after filtering in treatment: 28607911 INFO @ Sun, 21 Jun 2020 20:29:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:20: #2 number of paired peaks: 702 WARNING @ Sun, 21 Jun 2020 20:29:20: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:20: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:21: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:21: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:21: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:21: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 20:29:21: #2 alternative fragment length(s) may be 4,138 bps INFO @ Sun, 21 Jun 2020 20:29:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.20_model.r INFO @ Sun, 21 Jun 2020 20:29:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.05_summits.bed INFO @ Sun, 21 Jun 2020 20:29:48: Done! pass1 - making usageList (215 chroms): 2 millis pass2 - checking and writing primary data (10779 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:30:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.10_summits.bed INFO @ Sun, 21 Jun 2020 20:30:44: Done! pass1 - making usageList (163 chroms): 2 millis pass2 - checking and writing primary data (6450 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:30:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981628/SRX3981628.20_summits.bed INFO @ Sun, 21 Jun 2020 20:30:54: Done! pass1 - making usageList (119 chroms): 1 millis pass2 - checking and writing primary data (2597 records, 4 fields): 7 millis CompletedMACS2peakCalling