Job ID = 6454958 SRX = SRX2618501 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:42:40 prefetch.2.10.7: 1) Downloading 'SRR5319055'... 2020-06-21T09:42:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:57 prefetch.2.10.7: 1) 'SRR5319055' was downloaded successfully 2020-06-21T09:46:57 prefetch.2.10.7: 'SRR5319055' has 0 unresolved dependencies Read 45288360 spots for SRR5319055/SRR5319055.sra Written 45288360 spots for SRR5319055/SRR5319055.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:06 45288360 reads; of these: 45288360 (100.00%) were unpaired; of these: 21691244 (47.90%) aligned 0 times 20184977 (44.57%) aligned exactly 1 time 3412139 (7.53%) aligned >1 times 52.10% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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 12 files... [bam_rmdupse_core] 3058375 / 23597116 = 0.1296 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 19:02:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.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 19:02:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:46: 1000000 INFO @ Sun, 21 Jun 2020 19:02:53: 2000000 INFO @ Sun, 21 Jun 2020 19:03:00: 3000000 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 19:03:07: 4000000 INFO @ Sun, 21 Jun 2020 19:03:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.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 19:03:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:15: 5000000 INFO @ Sun, 21 Jun 2020 19:03:17: 1000000 INFO @ Sun, 21 Jun 2020 19:03:23: 6000000 INFO @ Sun, 21 Jun 2020 19:03:25: 2000000 INFO @ Sun, 21 Jun 2020 19:03:31: 7000000 INFO @ Sun, 21 Jun 2020 19:03:32: 3000000 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 19:03:39: 8000000 INFO @ Sun, 21 Jun 2020 19:03:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.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 19:03:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:40: 4000000 INFO @ Sun, 21 Jun 2020 19:03:47: 9000000 INFO @ Sun, 21 Jun 2020 19:03:48: 1000000 INFO @ Sun, 21 Jun 2020 19:03:48: 5000000 INFO @ Sun, 21 Jun 2020 19:03:55: 10000000 INFO @ Sun, 21 Jun 2020 19:03:56: 6000000 INFO @ Sun, 21 Jun 2020 19:03:56: 2000000 INFO @ Sun, 21 Jun 2020 19:04:03: 11000000 INFO @ Sun, 21 Jun 2020 19:04:03: 7000000 INFO @ Sun, 21 Jun 2020 19:04:04: 3000000 INFO @ Sun, 21 Jun 2020 19:04:11: 8000000 INFO @ Sun, 21 Jun 2020 19:04:11: 12000000 INFO @ Sun, 21 Jun 2020 19:04:13: 4000000 INFO @ Sun, 21 Jun 2020 19:04:19: 9000000 INFO @ Sun, 21 Jun 2020 19:04:19: 13000000 INFO @ Sun, 21 Jun 2020 19:04:21: 5000000 INFO @ Sun, 21 Jun 2020 19:04:26: 10000000 INFO @ Sun, 21 Jun 2020 19:04:27: 14000000 INFO @ Sun, 21 Jun 2020 19:04:29: 6000000 INFO @ Sun, 21 Jun 2020 19:04:34: 11000000 INFO @ Sun, 21 Jun 2020 19:04:36: 15000000 INFO @ Sun, 21 Jun 2020 19:04:37: 7000000 INFO @ Sun, 21 Jun 2020 19:04:42: 12000000 INFO @ Sun, 21 Jun 2020 19:04:44: 16000000 INFO @ Sun, 21 Jun 2020 19:04:45: 8000000 INFO @ Sun, 21 Jun 2020 19:04:50: 13000000 INFO @ Sun, 21 Jun 2020 19:04:52: 17000000 INFO @ Sun, 21 Jun 2020 19:04:54: 9000000 INFO @ Sun, 21 Jun 2020 19:04:57: 14000000 INFO @ Sun, 21 Jun 2020 19:05:00: 18000000 INFO @ Sun, 21 Jun 2020 19:05:02: 10000000 INFO @ Sun, 21 Jun 2020 19:05:05: 15000000 INFO @ Sun, 21 Jun 2020 19:05:09: 19000000 INFO @ Sun, 21 Jun 2020 19:05:10: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:05:13: 16000000 INFO @ Sun, 21 Jun 2020 19:05:17: 20000000 INFO @ Sun, 21 Jun 2020 19:05:18: 12000000 INFO @ Sun, 21 Jun 2020 19:05:21: 17000000 INFO @ Sun, 21 Jun 2020 19:05:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:05:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:05:21: #1 total tags in treatment: 20538741 INFO @ Sun, 21 Jun 2020 19:05:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:21: #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 19:05:22: #1 tags after filtering in treatment: 20538736 INFO @ Sun, 21 Jun 2020 19:05:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:23: #2 number of paired peaks: 473 WARNING @ Sun, 21 Jun 2020 19:05:23: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:23: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 19:05:23: #2 alternative fragment length(s) may be 3,102 bps INFO @ Sun, 21 Jun 2020 19:05:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.05_model.r INFO @ Sun, 21 Jun 2020 19:05:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:26: 13000000 INFO @ Sun, 21 Jun 2020 19:05:28: 18000000 INFO @ Sun, 21 Jun 2020 19:05:34: 14000000 INFO @ Sun, 21 Jun 2020 19:05:36: 19000000 INFO @ Sun, 21 Jun 2020 19:05:42: 15000000 INFO @ Sun, 21 Jun 2020 19:05:43: 20000000 INFO @ Sun, 21 Jun 2020 19:05:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:05:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:05:48: #1 total tags in treatment: 20538741 INFO @ Sun, 21 Jun 2020 19:05:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:48: #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 19:05:48: #1 tags after filtering in treatment: 20538736 INFO @ Sun, 21 Jun 2020 19:05:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:50: #2 number of paired peaks: 473 WARNING @ Sun, 21 Jun 2020 19:05:50: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:50: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 19:05:50: #2 alternative fragment length(s) may be 3,102 bps INFO @ Sun, 21 Jun 2020 19:05:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.10_model.r INFO @ Sun, 21 Jun 2020 19:05:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:50: 16000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:05:58: 17000000 INFO @ Sun, 21 Jun 2020 19:06:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:05: 18000000 INFO @ Sun, 21 Jun 2020 19:06:13: 19000000 INFO @ Sun, 21 Jun 2020 19:06:20: 20000000 INFO @ Sun, 21 Jun 2020 19:06:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:24: #1 total tags in treatment: 20538741 INFO @ Sun, 21 Jun 2020 19:06:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:24: #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 19:06:24: #1 tags after filtering in treatment: 20538736 INFO @ Sun, 21 Jun 2020 19:06:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:26: #2 number of paired peaks: 473 WARNING @ Sun, 21 Jun 2020 19:06:26: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Sun, 21 Jun 2020 19:06:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:26: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 19:06:26: #2 alternative fragment length(s) may be 3,102 bps INFO @ Sun, 21 Jun 2020 19:06:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.20_model.r INFO @ Sun, 21 Jun 2020 19:06:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.05_summits.bed INFO @ Sun, 21 Jun 2020 19:06:26: Done! pass1 - making usageList (479 chroms): 2 millis pass2 - checking and writing primary data (8332 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:06:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.10_summits.bed INFO @ Sun, 21 Jun 2020 19:06:51: Done! pass1 - making usageList (444 chroms): 2 millis pass2 - checking and writing primary data (4621 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:07:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618501/SRX2618501.20_summits.bed INFO @ Sun, 21 Jun 2020 19:07:26: Done! pass1 - making usageList (403 chroms): 1 millis pass2 - checking and writing primary data (1756 records, 4 fields): 12 millis CompletedMACS2peakCalling