Job ID = 6454202 SRX = SRX1872289 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:06:09 prefetch.2.10.7: 1) Downloading 'SRR3712750'... 2020-06-21T09:06:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:13:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:13:26 prefetch.2.10.7: 1) 'SRR3712750' was downloaded successfully Read 40997558 spots for SRR3712750/SRR3712750.sra Written 40997558 spots for SRR3712750/SRR3712750.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: 00:08:45 40997558 reads; of these: 40997558 (100.00%) were unpaired; of these: 4996467 (12.19%) aligned 0 times 31580634 (77.03%) aligned exactly 1 time 4420457 (10.78%) aligned >1 times 87.81% overall alignment rate Time searching: 00:08:45 Overall time: 00:08:45 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] 6282894 / 36001091 = 0.1745 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 18:32:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.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 18:32:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:43: 1000000 INFO @ Sun, 21 Jun 2020 18:32:47: 2000000 INFO @ Sun, 21 Jun 2020 18:32:52: 3000000 INFO @ Sun, 21 Jun 2020 18:32:57: 4000000 INFO @ Sun, 21 Jun 2020 18:33:02: 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 18:33:06: 6000000 INFO @ Sun, 21 Jun 2020 18:33:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.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 18:33:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:11: 7000000 INFO @ Sun, 21 Jun 2020 18:33:13: 1000000 INFO @ Sun, 21 Jun 2020 18:33:16: 8000000 INFO @ Sun, 21 Jun 2020 18:33:18: 2000000 INFO @ Sun, 21 Jun 2020 18:33:21: 9000000 INFO @ Sun, 21 Jun 2020 18:33:24: 3000000 INFO @ Sun, 21 Jun 2020 18:33:26: 10000000 INFO @ Sun, 21 Jun 2020 18:33:30: 4000000 INFO @ Sun, 21 Jun 2020 18:33:31: 11000000 INFO @ Sun, 21 Jun 2020 18:33:36: 12000000 INFO @ Sun, 21 Jun 2020 18:33:36: 5000000 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 18:33:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.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 18:33:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:41: 13000000 INFO @ Sun, 21 Jun 2020 18:33:42: 6000000 INFO @ Sun, 21 Jun 2020 18:33:43: 1000000 INFO @ Sun, 21 Jun 2020 18:33:46: 14000000 INFO @ Sun, 21 Jun 2020 18:33:47: 7000000 INFO @ Sun, 21 Jun 2020 18:33:49: 2000000 INFO @ Sun, 21 Jun 2020 18:33:50: 15000000 INFO @ Sun, 21 Jun 2020 18:33:53: 8000000 INFO @ Sun, 21 Jun 2020 18:33:55: 3000000 INFO @ Sun, 21 Jun 2020 18:33:55: 16000000 INFO @ Sun, 21 Jun 2020 18:33:58: 9000000 INFO @ Sun, 21 Jun 2020 18:34:00: 17000000 INFO @ Sun, 21 Jun 2020 18:34:00: 4000000 INFO @ Sun, 21 Jun 2020 18:34:04: 10000000 INFO @ Sun, 21 Jun 2020 18:34:05: 18000000 INFO @ Sun, 21 Jun 2020 18:34:06: 5000000 INFO @ Sun, 21 Jun 2020 18:34:09: 11000000 INFO @ Sun, 21 Jun 2020 18:34:10: 19000000 INFO @ Sun, 21 Jun 2020 18:34:12: 6000000 INFO @ Sun, 21 Jun 2020 18:34:15: 20000000 INFO @ Sun, 21 Jun 2020 18:34:15: 12000000 INFO @ Sun, 21 Jun 2020 18:34:18: 7000000 INFO @ Sun, 21 Jun 2020 18:34:20: 21000000 INFO @ Sun, 21 Jun 2020 18:34:21: 13000000 INFO @ Sun, 21 Jun 2020 18:34:23: 8000000 INFO @ Sun, 21 Jun 2020 18:34:25: 22000000 INFO @ Sun, 21 Jun 2020 18:34:27: 14000000 INFO @ Sun, 21 Jun 2020 18:34:29: 9000000 INFO @ Sun, 21 Jun 2020 18:34:30: 23000000 INFO @ Sun, 21 Jun 2020 18:34:32: 15000000 INFO @ Sun, 21 Jun 2020 18:34:34: 10000000 INFO @ Sun, 21 Jun 2020 18:34:35: 24000000 INFO @ Sun, 21 Jun 2020 18:34:38: 16000000 INFO @ Sun, 21 Jun 2020 18:34:40: 11000000 INFO @ Sun, 21 Jun 2020 18:34:40: 25000000 INFO @ Sun, 21 Jun 2020 18:34:44: 17000000 INFO @ Sun, 21 Jun 2020 18:34:45: 26000000 INFO @ Sun, 21 Jun 2020 18:34:45: 12000000 INFO @ Sun, 21 Jun 2020 18:34:49: 18000000 INFO @ Sun, 21 Jun 2020 18:34:50: 27000000 INFO @ Sun, 21 Jun 2020 18:34:51: 13000000 INFO @ Sun, 21 Jun 2020 18:34:55: 19000000 INFO @ Sun, 21 Jun 2020 18:34:55: 28000000 INFO @ Sun, 21 Jun 2020 18:34:57: 14000000 INFO @ Sun, 21 Jun 2020 18:35:00: 29000000 INFO @ Sun, 21 Jun 2020 18:35:00: 20000000 INFO @ Sun, 21 Jun 2020 18:35:03: 15000000 INFO @ Sun, 21 Jun 2020 18:35:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:35:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:35:04: #1 total tags in treatment: 29718197 INFO @ Sun, 21 Jun 2020 18:35:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:04: #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 18:35:04: #1 tags after filtering in treatment: 29718197 INFO @ Sun, 21 Jun 2020 18:35:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:06: 21000000 INFO @ Sun, 21 Jun 2020 18:35:06: #2 number of paired peaks: 157 WARNING @ Sun, 21 Jun 2020 18:35:06: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sun, 21 Jun 2020 18:35:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:06: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 18:35:06: #2 alternative fragment length(s) may be 3,163,188 bps INFO @ Sun, 21 Jun 2020 18:35:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.05_model.r INFO @ Sun, 21 Jun 2020 18:35:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:08: 16000000 INFO @ Sun, 21 Jun 2020 18:35:11: 22000000 INFO @ Sun, 21 Jun 2020 18:35:14: 17000000 INFO @ Sun, 21 Jun 2020 18:35:17: 23000000 INFO @ Sun, 21 Jun 2020 18:35:20: 18000000 INFO @ Sun, 21 Jun 2020 18:35:23: 24000000 INFO @ Sun, 21 Jun 2020 18:35:25: 19000000 INFO @ Sun, 21 Jun 2020 18:35:29: 25000000 INFO @ Sun, 21 Jun 2020 18:35:31: 20000000 INFO @ Sun, 21 Jun 2020 18:35:34: 26000000 INFO @ Sun, 21 Jun 2020 18:35:36: 21000000 INFO @ Sun, 21 Jun 2020 18:35:40: 27000000 INFO @ Sun, 21 Jun 2020 18:35:42: 22000000 INFO @ Sun, 21 Jun 2020 18:35:46: 28000000 INFO @ Sun, 21 Jun 2020 18:35:48: 23000000 INFO @ Sun, 21 Jun 2020 18:35:51: 29000000 INFO @ Sun, 21 Jun 2020 18:35:53: 24000000 INFO @ Sun, 21 Jun 2020 18:35:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:35:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:35:56: #1 total tags in treatment: 29718197 INFO @ Sun, 21 Jun 2020 18:35:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:56: #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 18:35:56: #1 tags after filtering in treatment: 29718197 INFO @ Sun, 21 Jun 2020 18:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:58: #2 number of paired peaks: 157 WARNING @ Sun, 21 Jun 2020 18:35:58: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sun, 21 Jun 2020 18:35:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:59: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 18:35:59: #2 alternative fragment length(s) may be 3,163,188 bps INFO @ Sun, 21 Jun 2020 18:35:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.10_model.r INFO @ Sun, 21 Jun 2020 18:35:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:59: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:36:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:05: 26000000 INFO @ Sun, 21 Jun 2020 18:36:11: 27000000 INFO @ Sun, 21 Jun 2020 18:36:16: 28000000 INFO @ Sun, 21 Jun 2020 18:36:22: 29000000 INFO @ Sun, 21 Jun 2020 18:36:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:36:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:36:26: #1 total tags in treatment: 29718197 INFO @ Sun, 21 Jun 2020 18:36:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:26: #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 18:36:27: #1 tags after filtering in treatment: 29718197 INFO @ Sun, 21 Jun 2020 18:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.05_summits.bed INFO @ Sun, 21 Jun 2020 18:36:27: Done! pass1 - making usageList (167 chroms): 1 millis pass2 - checking and writing primary data (1355 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:36:29: #2 number of paired peaks: 157 WARNING @ Sun, 21 Jun 2020 18:36:29: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sun, 21 Jun 2020 18:36:29: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:29: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:29: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:29: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:29: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 18:36:29: #2 alternative fragment length(s) may be 3,163,188 bps INFO @ Sun, 21 Jun 2020 18:36:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.20_model.r INFO @ Sun, 21 Jun 2020 18:36:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:37:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.10_summits.bed INFO @ Sun, 21 Jun 2020 18:37:19: Done! pass1 - making usageList (106 chroms): 1 millis pass2 - checking and writing primary data (514 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:37:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1872289/SRX1872289.20_summits.bed INFO @ Sun, 21 Jun 2020 18:37:51: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (238 records, 4 fields): 4 millis CompletedMACS2peakCalling