Job ID = 6454751 SRX = SRX2564136 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:36:25 prefetch.2.10.7: 1) Downloading 'SRR5259255'... 2020-06-21T09:36:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:43:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:43:31 prefetch.2.10.7: 1) 'SRR5259255' was downloaded successfully 2020-06-21T09:43:31 prefetch.2.10.7: 'SRR5259255' has 0 unresolved dependencies Read 35080567 spots for SRR5259255/SRR5259255.sra Written 35080567 spots for SRR5259255/SRR5259255.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: 00:10:35 35080567 reads; of these: 35080567 (100.00%) were unpaired; of these: 5903545 (16.83%) aligned 0 times 25484884 (72.65%) aligned exactly 1 time 3692138 (10.52%) aligned >1 times 83.17% overall alignment rate Time searching: 00:10:35 Overall time: 00:10:35 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] 6384890 / 29177022 = 0.2188 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 19:07:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.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 19:07:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:14: 1000000 INFO @ Sun, 21 Jun 2020 19:07:21: 2000000 INFO @ Sun, 21 Jun 2020 19:07:28: 3000000 INFO @ Sun, 21 Jun 2020 19:07:35: 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 19:07:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.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 19:07:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:42: 5000000 INFO @ Sun, 21 Jun 2020 19:07:46: 1000000 INFO @ Sun, 21 Jun 2020 19:07:50: 6000000 INFO @ Sun, 21 Jun 2020 19:07:53: 2000000 INFO @ Sun, 21 Jun 2020 19:07:57: 7000000 INFO @ Sun, 21 Jun 2020 19:08:01: 3000000 INFO @ Sun, 21 Jun 2020 19:08:04: 8000000 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 19:08:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.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 19:08:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:08: 4000000 INFO @ Sun, 21 Jun 2020 19:08:12: 9000000 INFO @ Sun, 21 Jun 2020 19:08:15: 1000000 INFO @ Sun, 21 Jun 2020 19:08:16: 5000000 INFO @ Sun, 21 Jun 2020 19:08:19: 10000000 INFO @ Sun, 21 Jun 2020 19:08:23: 2000000 INFO @ Sun, 21 Jun 2020 19:08:24: 6000000 INFO @ Sun, 21 Jun 2020 19:08:27: 11000000 INFO @ Sun, 21 Jun 2020 19:08:30: 3000000 INFO @ Sun, 21 Jun 2020 19:08:31: 7000000 INFO @ Sun, 21 Jun 2020 19:08:35: 12000000 INFO @ Sun, 21 Jun 2020 19:08:38: 4000000 INFO @ Sun, 21 Jun 2020 19:08:39: 8000000 INFO @ Sun, 21 Jun 2020 19:08:42: 13000000 INFO @ Sun, 21 Jun 2020 19:08:46: 5000000 INFO @ Sun, 21 Jun 2020 19:08:46: 9000000 INFO @ Sun, 21 Jun 2020 19:08:50: 14000000 INFO @ Sun, 21 Jun 2020 19:08:53: 6000000 INFO @ Sun, 21 Jun 2020 19:08:54: 10000000 INFO @ Sun, 21 Jun 2020 19:08:57: 15000000 INFO @ Sun, 21 Jun 2020 19:09:01: 7000000 INFO @ Sun, 21 Jun 2020 19:09:02: 11000000 INFO @ Sun, 21 Jun 2020 19:09:05: 16000000 INFO @ Sun, 21 Jun 2020 19:09:09: 8000000 INFO @ Sun, 21 Jun 2020 19:09:09: 12000000 INFO @ Sun, 21 Jun 2020 19:09:12: 17000000 INFO @ Sun, 21 Jun 2020 19:09:16: 9000000 INFO @ Sun, 21 Jun 2020 19:09:17: 13000000 INFO @ Sun, 21 Jun 2020 19:09:20: 18000000 INFO @ Sun, 21 Jun 2020 19:09:24: 10000000 INFO @ Sun, 21 Jun 2020 19:09:24: 14000000 INFO @ Sun, 21 Jun 2020 19:09:28: 19000000 INFO @ Sun, 21 Jun 2020 19:09:32: 11000000 INFO @ Sun, 21 Jun 2020 19:09:32: 15000000 INFO @ Sun, 21 Jun 2020 19:09:36: 20000000 INFO @ Sun, 21 Jun 2020 19:09:40: 12000000 INFO @ Sun, 21 Jun 2020 19:09:40: 16000000 INFO @ Sun, 21 Jun 2020 19:09:44: 21000000 INFO @ Sun, 21 Jun 2020 19:09:48: 17000000 INFO @ Sun, 21 Jun 2020 19:09:48: 13000000 INFO @ Sun, 21 Jun 2020 19:09:51: 22000000 INFO @ Sun, 21 Jun 2020 19:09:55: 14000000 INFO @ Sun, 21 Jun 2020 19:09:55: 18000000 INFO @ Sun, 21 Jun 2020 19:09:58: #1 tag size is determined as 72 bps INFO @ Sun, 21 Jun 2020 19:09:58: #1 tag size = 72 INFO @ Sun, 21 Jun 2020 19:09:58: #1 total tags in treatment: 22792132 INFO @ Sun, 21 Jun 2020 19:09:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:58: #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 19:09:58: #1 tags after filtering in treatment: 22792129 INFO @ Sun, 21 Jun 2020 19:09:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:58: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:10:00: #2 number of paired peaks: 833 WARNING @ Sun, 21 Jun 2020 19:10:00: Fewer paired peaks (833) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 833 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:00: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 19:10:00: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 19:10:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.05_model.r INFO @ Sun, 21 Jun 2020 19:10:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:03: 15000000 INFO @ Sun, 21 Jun 2020 19:10:03: 19000000 INFO @ Sun, 21 Jun 2020 19:10:10: 16000000 INFO @ Sun, 21 Jun 2020 19:10:11: 20000000 INFO @ Sun, 21 Jun 2020 19:10:18: 17000000 INFO @ Sun, 21 Jun 2020 19:10:18: 21000000 INFO @ Sun, 21 Jun 2020 19:10:25: 18000000 INFO @ Sun, 21 Jun 2020 19:10:26: 22000000 INFO @ Sun, 21 Jun 2020 19:10:32: #1 tag size is determined as 72 bps INFO @ Sun, 21 Jun 2020 19:10:32: #1 tag size = 72 INFO @ Sun, 21 Jun 2020 19:10:32: #1 total tags in treatment: 22792132 INFO @ Sun, 21 Jun 2020 19:10:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:32: #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 19:10:33: #1 tags after filtering in treatment: 22792129 INFO @ Sun, 21 Jun 2020 19:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:34: 19000000 INFO @ Sun, 21 Jun 2020 19:10:34: #2 number of paired peaks: 833 WARNING @ Sun, 21 Jun 2020 19:10:34: Fewer paired peaks (833) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 833 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:35: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:35: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:35: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:35: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 19:10:35: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 19:10:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.10_model.r INFO @ Sun, 21 Jun 2020 19:10:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:41: 20000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:10:48: 21000000 INFO @ Sun, 21 Jun 2020 19:10:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:55: 22000000 INFO @ Sun, 21 Jun 2020 19:11:00: #1 tag size is determined as 72 bps INFO @ Sun, 21 Jun 2020 19:11:00: #1 tag size = 72 INFO @ Sun, 21 Jun 2020 19:11:00: #1 total tags in treatment: 22792132 INFO @ Sun, 21 Jun 2020 19:11:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:00: #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 19:11:01: #1 tags after filtering in treatment: 22792129 INFO @ Sun, 21 Jun 2020 19:11:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:01: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:03: #2 number of paired peaks: 833 WARNING @ Sun, 21 Jun 2020 19:11:03: Fewer paired peaks (833) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 833 pairs to build model! INFO @ Sun, 21 Jun 2020 19:11:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:03: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 19:11:03: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 19:11:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.20_model.r INFO @ Sun, 21 Jun 2020 19:11:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.05_summits.bed INFO @ Sun, 21 Jun 2020 19:11:14: Done! pass1 - making usageList (470 chroms): 3 millis pass2 - checking and writing primary data (10359 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:11:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.10_summits.bed INFO @ Sun, 21 Jun 2020 19:11:50: Done! pass1 - making usageList (428 chroms): 2 millis pass2 - checking and writing primary data (7757 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:11:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564136/SRX2564136.20_summits.bed INFO @ Sun, 21 Jun 2020 19:12:15: Done! pass1 - making usageList (344 chroms): 1 millis pass2 - checking and writing primary data (4922 records, 4 fields): 15 millis CompletedMACS2peakCalling