Job ID = 6456715 SRX = SRX3981622 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:00:16 prefetch.2.10.7: 1) Downloading 'SRR7050250'... 2020-06-21T11:00:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:01:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:01:42 prefetch.2.10.7: 'SRR7050250' is valid 2020-06-21T11:01:42 prefetch.2.10.7: 1) 'SRR7050250' was downloaded successfully 2020-06-21T11:01:42 prefetch.2.10.7: 'SRR7050250' has 0 unresolved dependencies Read 12886723 spots for SRR7050250/SRR7050250.sra Written 12886723 spots for SRR7050250/SRR7050250.sra 2020-06-21T11:02:32 prefetch.2.10.7: 1) Downloading 'SRR7050251'... 2020-06-21T11:02:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:03:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:03:50 prefetch.2.10.7: 'SRR7050251' is valid 2020-06-21T11:03:50 prefetch.2.10.7: 1) 'SRR7050251' was downloaded successfully 2020-06-21T11:03:50 prefetch.2.10.7: 'SRR7050251' has 0 unresolved dependencies Read 12700490 spots for SRR7050251/SRR7050251.sra Written 12700490 spots for SRR7050251/SRR7050251.sra 2020-06-21T11:04:40 prefetch.2.10.7: 1) Downloading 'SRR7050252'... 2020-06-21T11:04:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:06:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:06:26 prefetch.2.10.7: 'SRR7050252' is valid 2020-06-21T11:06:26 prefetch.2.10.7: 1) 'SRR7050252' was downloaded successfully 2020-06-21T11:06:26 prefetch.2.10.7: 'SRR7050252' has 0 unresolved dependencies Read 12865808 spots for SRR7050252/SRR7050252.sra Written 12865808 spots for SRR7050252/SRR7050252.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: 00:09:21 38453021 reads; of these: 38453021 (100.00%) were unpaired; of these: 1493923 (3.89%) aligned 0 times 29804402 (77.51%) aligned exactly 1 time 7154696 (18.61%) aligned >1 times 96.11% overall alignment rate Time searching: 00:09:21 Overall time: 00:09:21 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] 6317390 / 36959098 = 0.1709 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 20:24:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.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 20:24:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:08: 1000000 INFO @ Sun, 21 Jun 2020 20:24:12: 2000000 INFO @ Sun, 21 Jun 2020 20:24:17: 3000000 INFO @ Sun, 21 Jun 2020 20:24:21: 4000000 INFO @ Sun, 21 Jun 2020 20:24:26: 5000000 INFO @ Sun, 21 Jun 2020 20:24:31: 6000000 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 20:24:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.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 20:24:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:35: 7000000 INFO @ Sun, 21 Jun 2020 20:24:38: 1000000 INFO @ Sun, 21 Jun 2020 20:24:40: 8000000 INFO @ Sun, 21 Jun 2020 20:24:43: 2000000 INFO @ Sun, 21 Jun 2020 20:24:45: 9000000 INFO @ Sun, 21 Jun 2020 20:24:48: 3000000 INFO @ Sun, 21 Jun 2020 20:24:50: 10000000 INFO @ Sun, 21 Jun 2020 20:24:53: 4000000 INFO @ Sun, 21 Jun 2020 20:24:55: 11000000 INFO @ Sun, 21 Jun 2020 20:24:58: 5000000 INFO @ Sun, 21 Jun 2020 20:24:59: 12000000 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 20:25:02: 6000000 INFO @ Sun, 21 Jun 2020 20:25:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.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 20:25:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:04: 13000000 INFO @ Sun, 21 Jun 2020 20:25:07: 7000000 INFO @ Sun, 21 Jun 2020 20:25:08: 1000000 INFO @ Sun, 21 Jun 2020 20:25:09: 14000000 INFO @ Sun, 21 Jun 2020 20:25:12: 8000000 INFO @ Sun, 21 Jun 2020 20:25:13: 2000000 INFO @ Sun, 21 Jun 2020 20:25:14: 15000000 INFO @ Sun, 21 Jun 2020 20:25:17: 9000000 INFO @ Sun, 21 Jun 2020 20:25:18: 3000000 INFO @ Sun, 21 Jun 2020 20:25:19: 16000000 INFO @ Sun, 21 Jun 2020 20:25:22: 10000000 INFO @ Sun, 21 Jun 2020 20:25:23: 4000000 INFO @ Sun, 21 Jun 2020 20:25:24: 17000000 INFO @ Sun, 21 Jun 2020 20:25:27: 11000000 INFO @ Sun, 21 Jun 2020 20:25:28: 5000000 INFO @ Sun, 21 Jun 2020 20:25:28: 18000000 INFO @ Sun, 21 Jun 2020 20:25:32: 12000000 INFO @ Sun, 21 Jun 2020 20:25:33: 6000000 INFO @ Sun, 21 Jun 2020 20:25:33: 19000000 INFO @ Sun, 21 Jun 2020 20:25:37: 13000000 INFO @ Sun, 21 Jun 2020 20:25:38: 7000000 INFO @ Sun, 21 Jun 2020 20:25:38: 20000000 INFO @ Sun, 21 Jun 2020 20:25:42: 14000000 INFO @ Sun, 21 Jun 2020 20:25:42: 8000000 INFO @ Sun, 21 Jun 2020 20:25:43: 21000000 INFO @ Sun, 21 Jun 2020 20:25:46: 15000000 INFO @ Sun, 21 Jun 2020 20:25:47: 9000000 INFO @ Sun, 21 Jun 2020 20:25:48: 22000000 INFO @ Sun, 21 Jun 2020 20:25:51: 16000000 INFO @ Sun, 21 Jun 2020 20:25:52: 10000000 INFO @ Sun, 21 Jun 2020 20:25:52: 23000000 INFO @ Sun, 21 Jun 2020 20:25:56: 17000000 INFO @ Sun, 21 Jun 2020 20:25:57: 24000000 INFO @ Sun, 21 Jun 2020 20:25:57: 11000000 INFO @ Sun, 21 Jun 2020 20:26:01: 18000000 INFO @ Sun, 21 Jun 2020 20:26:02: 25000000 INFO @ Sun, 21 Jun 2020 20:26:02: 12000000 INFO @ Sun, 21 Jun 2020 20:26:07: 19000000 INFO @ Sun, 21 Jun 2020 20:26:07: 26000000 INFO @ Sun, 21 Jun 2020 20:26:07: 13000000 INFO @ Sun, 21 Jun 2020 20:26:12: 20000000 INFO @ Sun, 21 Jun 2020 20:26:12: 14000000 INFO @ Sun, 21 Jun 2020 20:26:12: 27000000 INFO @ Sun, 21 Jun 2020 20:26:17: 21000000 INFO @ Sun, 21 Jun 2020 20:26:17: 15000000 INFO @ Sun, 21 Jun 2020 20:26:17: 28000000 INFO @ Sun, 21 Jun 2020 20:26:22: 16000000 INFO @ Sun, 21 Jun 2020 20:26:22: 22000000 INFO @ Sun, 21 Jun 2020 20:26:22: 29000000 INFO @ Sun, 21 Jun 2020 20:26:27: 17000000 INFO @ Sun, 21 Jun 2020 20:26:27: 30000000 INFO @ Sun, 21 Jun 2020 20:26:27: 23000000 INFO @ Sun, 21 Jun 2020 20:26:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:26:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:26:31: #1 total tags in treatment: 30641708 INFO @ Sun, 21 Jun 2020 20:26:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:26:31: #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 20:26:31: #1 tags after filtering in treatment: 30641653 INFO @ Sun, 21 Jun 2020 20:26:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:26:31: #1 finished! INFO @ Sun, 21 Jun 2020 20:26:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:26:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:26:31: 18000000 INFO @ Sun, 21 Jun 2020 20:26:33: 24000000 INFO @ Sun, 21 Jun 2020 20:26:33: #2 number of paired peaks: 496 WARNING @ Sun, 21 Jun 2020 20:26:33: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Sun, 21 Jun 2020 20:26:33: start model_add_line... INFO @ Sun, 21 Jun 2020 20:26:34: start X-correlation... INFO @ Sun, 21 Jun 2020 20:26:34: end of X-cor INFO @ Sun, 21 Jun 2020 20:26:34: #2 finished! INFO @ Sun, 21 Jun 2020 20:26:34: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 20:26:34: #2 alternative fragment length(s) may be 4,137 bps INFO @ Sun, 21 Jun 2020 20:26:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.05_model.r INFO @ Sun, 21 Jun 2020 20:26:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:26:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:26:36: 19000000 INFO @ Sun, 21 Jun 2020 20:26:38: 25000000 INFO @ Sun, 21 Jun 2020 20:26:41: 20000000 INFO @ Sun, 21 Jun 2020 20:26:44: 26000000 INFO @ Sun, 21 Jun 2020 20:26:46: 21000000 INFO @ Sun, 21 Jun 2020 20:26:50: 27000000 INFO @ Sun, 21 Jun 2020 20:26:51: 22000000 INFO @ Sun, 21 Jun 2020 20:26:55: 28000000 INFO @ Sun, 21 Jun 2020 20:26:56: 23000000 INFO @ Sun, 21 Jun 2020 20:27:00: 24000000 INFO @ Sun, 21 Jun 2020 20:27:01: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:27:05: 25000000 INFO @ Sun, 21 Jun 2020 20:27:06: 30000000 INFO @ Sun, 21 Jun 2020 20:27:10: 26000000 INFO @ Sun, 21 Jun 2020 20:27:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:27:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:27:11: #1 total tags in treatment: 30641708 INFO @ Sun, 21 Jun 2020 20:27:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:11: #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 20:27:11: #1 tags after filtering in treatment: 30641653 INFO @ Sun, 21 Jun 2020 20:27:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:11: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:13: #2 number of paired peaks: 496 WARNING @ Sun, 21 Jun 2020 20:27:13: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Sun, 21 Jun 2020 20:27:13: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:14: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 20:27:14: #2 alternative fragment length(s) may be 4,137 bps INFO @ Sun, 21 Jun 2020 20:27:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.10_model.r INFO @ Sun, 21 Jun 2020 20:27:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:27:15: 27000000 INFO @ Sun, 21 Jun 2020 20:27:20: 28000000 INFO @ Sun, 21 Jun 2020 20:27:24: 29000000 INFO @ Sun, 21 Jun 2020 20:27:29: 30000000 INFO @ Sun, 21 Jun 2020 20:27:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:27:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:27:33: #1 total tags in treatment: 30641708 INFO @ Sun, 21 Jun 2020 20:27:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:33: #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 20:27:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:27:33: #1 tags after filtering in treatment: 30641653 INFO @ Sun, 21 Jun 2020 20:27:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:33: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:35: #2 number of paired peaks: 496 WARNING @ Sun, 21 Jun 2020 20:27:35: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Sun, 21 Jun 2020 20:27:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:36: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 20:27:36: #2 alternative fragment length(s) may be 4,137 bps INFO @ Sun, 21 Jun 2020 20:27:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.20_model.r INFO @ Sun, 21 Jun 2020 20:27:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:28:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:28:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:28:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.05_summits.bed INFO @ Sun, 21 Jun 2020 20:28:01: Done! pass1 - making usageList (239 chroms): 2 millis pass2 - checking and writing primary data (10701 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:28:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:28:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:28:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:28:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:28:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.10_summits.bed INFO @ Sun, 21 Jun 2020 20:28:41: Done! pass1 - making usageList (175 chroms): 1 millis pass2 - checking and writing primary data (6302 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981622/SRX3981622.20_summits.bed INFO @ Sun, 21 Jun 2020 20:29:05: Done! pass1 - making usageList (117 chroms): 2 millis pass2 - checking and writing primary data (2389 records, 4 fields): 6 millis CompletedMACS2peakCalling