Job ID = 6456791 SRX = SRX3981685 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:13:09 prefetch.2.10.7: 1) Downloading 'SRR7050439'... 2020-06-21T11:13:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:14:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:14:10 prefetch.2.10.7: 'SRR7050439' is valid 2020-06-21T11:14:10 prefetch.2.10.7: 1) 'SRR7050439' was downloaded successfully 2020-06-21T11:14:10 prefetch.2.10.7: 'SRR7050439' has 0 unresolved dependencies Read 13555512 spots for SRR7050439/SRR7050439.sra Written 13555512 spots for SRR7050439/SRR7050439.sra 2020-06-21T11:15:04 prefetch.2.10.7: 1) Downloading 'SRR7050440'... 2020-06-21T11:15:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:16:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:16:23 prefetch.2.10.7: 'SRR7050440' is valid 2020-06-21T11:16:23 prefetch.2.10.7: 1) 'SRR7050440' was downloaded successfully 2020-06-21T11:16:23 prefetch.2.10.7: 'SRR7050440' has 0 unresolved dependencies Read 13557217 spots for SRR7050440/SRR7050440.sra Written 13557217 spots for SRR7050440/SRR7050440.sra 2020-06-21T11:17:19 prefetch.2.10.7: 1) Downloading 'SRR7050441'... 2020-06-21T11:17:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:18:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:18:11 prefetch.2.10.7: 'SRR7050441' is valid 2020-06-21T11:18:11 prefetch.2.10.7: 1) 'SRR7050441' was downloaded successfully 2020-06-21T11:18:11 prefetch.2.10.7: 'SRR7050441' has 0 unresolved dependencies Read 13480358 spots for SRR7050441/SRR7050441.sra Written 13480358 spots for SRR7050441/SRR7050441.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: 00:10:28 40593087 reads; of these: 40593087 (100.00%) were unpaired; of these: 1215179 (2.99%) aligned 0 times 32769344 (80.73%) aligned exactly 1 time 6608564 (16.28%) aligned >1 times 97.01% overall alignment rate Time searching: 00:10:28 Overall time: 00:10:28 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 20 files... [bam_rmdupse_core] 7730711 / 39377908 = 0.1963 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 20:38:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.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 20:38:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:31: 1000000 INFO @ Sun, 21 Jun 2020 20:38:36: 2000000 INFO @ Sun, 21 Jun 2020 20:38:41: 3000000 INFO @ Sun, 21 Jun 2020 20:38:46: 4000000 INFO @ Sun, 21 Jun 2020 20:38:51: 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 20:38:56: 6000000 INFO @ Sun, 21 Jun 2020 20:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.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 20:38:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:01: 7000000 INFO @ Sun, 21 Jun 2020 20:39:02: 1000000 INFO @ Sun, 21 Jun 2020 20:39:06: 8000000 INFO @ Sun, 21 Jun 2020 20:39:07: 2000000 INFO @ Sun, 21 Jun 2020 20:39:11: 9000000 INFO @ Sun, 21 Jun 2020 20:39:12: 3000000 INFO @ Sun, 21 Jun 2020 20:39:17: 10000000 INFO @ Sun, 21 Jun 2020 20:39:17: 4000000 INFO @ Sun, 21 Jun 2020 20:39:22: 11000000 INFO @ Sun, 21 Jun 2020 20:39:23: 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 20:39:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.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 20:39:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:27: 12000000 INFO @ Sun, 21 Jun 2020 20:39:28: 6000000 INFO @ Sun, 21 Jun 2020 20:39:32: 1000000 INFO @ Sun, 21 Jun 2020 20:39:32: 13000000 INFO @ Sun, 21 Jun 2020 20:39:33: 7000000 INFO @ Sun, 21 Jun 2020 20:39:37: 2000000 INFO @ Sun, 21 Jun 2020 20:39:37: 14000000 INFO @ Sun, 21 Jun 2020 20:39:38: 8000000 INFO @ Sun, 21 Jun 2020 20:39:42: 15000000 INFO @ Sun, 21 Jun 2020 20:39:42: 3000000 INFO @ Sun, 21 Jun 2020 20:39:43: 9000000 INFO @ Sun, 21 Jun 2020 20:39:48: 4000000 INFO @ Sun, 21 Jun 2020 20:39:48: 16000000 INFO @ Sun, 21 Jun 2020 20:39:49: 10000000 INFO @ Sun, 21 Jun 2020 20:39:53: 5000000 INFO @ Sun, 21 Jun 2020 20:39:53: 17000000 INFO @ Sun, 21 Jun 2020 20:39:54: 11000000 INFO @ Sun, 21 Jun 2020 20:39:58: 18000000 INFO @ Sun, 21 Jun 2020 20:39:59: 6000000 INFO @ Sun, 21 Jun 2020 20:39:59: 12000000 INFO @ Sun, 21 Jun 2020 20:40:04: 19000000 INFO @ Sun, 21 Jun 2020 20:40:04: 7000000 INFO @ Sun, 21 Jun 2020 20:40:04: 13000000 INFO @ Sun, 21 Jun 2020 20:40:09: 20000000 INFO @ Sun, 21 Jun 2020 20:40:10: 8000000 INFO @ Sun, 21 Jun 2020 20:40:10: 14000000 INFO @ Sun, 21 Jun 2020 20:40:14: 21000000 INFO @ Sun, 21 Jun 2020 20:40:15: 9000000 INFO @ Sun, 21 Jun 2020 20:40:15: 15000000 INFO @ Sun, 21 Jun 2020 20:40:19: 22000000 INFO @ Sun, 21 Jun 2020 20:40:20: 10000000 INFO @ Sun, 21 Jun 2020 20:40:21: 16000000 INFO @ Sun, 21 Jun 2020 20:40:25: 23000000 INFO @ Sun, 21 Jun 2020 20:40:25: 11000000 INFO @ Sun, 21 Jun 2020 20:40:26: 17000000 INFO @ Sun, 21 Jun 2020 20:40:30: 24000000 INFO @ Sun, 21 Jun 2020 20:40:31: 12000000 INFO @ Sun, 21 Jun 2020 20:40:32: 18000000 INFO @ Sun, 21 Jun 2020 20:40:36: 25000000 INFO @ Sun, 21 Jun 2020 20:40:36: 13000000 INFO @ Sun, 21 Jun 2020 20:40:37: 19000000 INFO @ Sun, 21 Jun 2020 20:40:41: 26000000 INFO @ Sun, 21 Jun 2020 20:40:41: 14000000 INFO @ Sun, 21 Jun 2020 20:40:42: 20000000 INFO @ Sun, 21 Jun 2020 20:40:47: 15000000 INFO @ Sun, 21 Jun 2020 20:40:47: 27000000 INFO @ Sun, 21 Jun 2020 20:40:48: 21000000 INFO @ Sun, 21 Jun 2020 20:40:52: 16000000 INFO @ Sun, 21 Jun 2020 20:40:52: 28000000 INFO @ Sun, 21 Jun 2020 20:40:53: 22000000 INFO @ Sun, 21 Jun 2020 20:40:58: 29000000 INFO @ Sun, 21 Jun 2020 20:40:58: 17000000 INFO @ Sun, 21 Jun 2020 20:40:58: 23000000 INFO @ Sun, 21 Jun 2020 20:41:03: 30000000 INFO @ Sun, 21 Jun 2020 20:41:03: 18000000 INFO @ Sun, 21 Jun 2020 20:41:04: 24000000 INFO @ Sun, 21 Jun 2020 20:41:08: 31000000 INFO @ Sun, 21 Jun 2020 20:41:09: 19000000 INFO @ Sun, 21 Jun 2020 20:41:09: 25000000 INFO @ Sun, 21 Jun 2020 20:41:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:41:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:41:12: #1 total tags in treatment: 31647197 INFO @ Sun, 21 Jun 2020 20:41:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:12: #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 20:41:13: #1 tags after filtering in treatment: 31647125 INFO @ Sun, 21 Jun 2020 20:41:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:14: 20000000 INFO @ Sun, 21 Jun 2020 20:41:15: 26000000 INFO @ Sun, 21 Jun 2020 20:41:15: #2 number of paired peaks: 752 WARNING @ Sun, 21 Jun 2020 20:41:15: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Sun, 21 Jun 2020 20:41:15: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:16: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:16: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:16: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:16: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 20:41:16: #2 alternative fragment length(s) may be 4,130 bps INFO @ Sun, 21 Jun 2020 20:41:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.05_model.r INFO @ Sun, 21 Jun 2020 20:41:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:20: 21000000 INFO @ Sun, 21 Jun 2020 20:41:21: 27000000 INFO @ Sun, 21 Jun 2020 20:41:25: 22000000 INFO @ Sun, 21 Jun 2020 20:41:27: 28000000 INFO @ Sun, 21 Jun 2020 20:41:31: 23000000 INFO @ Sun, 21 Jun 2020 20:41:32: 29000000 INFO @ Sun, 21 Jun 2020 20:41:36: 24000000 INFO @ Sun, 21 Jun 2020 20:41:38: 30000000 INFO @ Sun, 21 Jun 2020 20:41:41: 25000000 INFO @ Sun, 21 Jun 2020 20:41:43: 31000000 INFO @ Sun, 21 Jun 2020 20:41:46: 26000000 INFO @ Sun, 21 Jun 2020 20:41:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:41:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:41:47: #1 total tags in treatment: 31647197 INFO @ Sun, 21 Jun 2020 20:41:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:47: #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 20:41:47: #1 tags after filtering in treatment: 31647125 INFO @ Sun, 21 Jun 2020 20:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:47: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:50: #2 number of paired peaks: 752 WARNING @ Sun, 21 Jun 2020 20:41:50: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Sun, 21 Jun 2020 20:41:50: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:50: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:50: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:50: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:50: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 20:41:50: #2 alternative fragment length(s) may be 4,130 bps INFO @ Sun, 21 Jun 2020 20:41:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.10_model.r INFO @ Sun, 21 Jun 2020 20:41:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:52: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:41:57: 28000000 INFO @ Sun, 21 Jun 2020 20:42:02: 29000000 INFO @ Sun, 21 Jun 2020 20:42:07: 30000000 INFO @ Sun, 21 Jun 2020 20:42:12: 31000000 INFO @ Sun, 21 Jun 2020 20:42:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:42:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:42:15: #1 total tags in treatment: 31647197 INFO @ Sun, 21 Jun 2020 20:42:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:15: #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 20:42:16: #1 tags after filtering in treatment: 31647125 INFO @ Sun, 21 Jun 2020 20:42:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:16: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:18: #2 number of paired peaks: 752 WARNING @ Sun, 21 Jun 2020 20:42:18: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Sun, 21 Jun 2020 20:42:18: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:19: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:19: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:19: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:19: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 20:42:19: #2 alternative fragment length(s) may be 4,130 bps INFO @ Sun, 21 Jun 2020 20:42:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.20_model.r INFO @ Sun, 21 Jun 2020 20:42:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:42:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:42:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:42:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.05_summits.bed INFO @ Sun, 21 Jun 2020 20:42:53: Done! pass1 - making usageList (261 chroms): 2 millis pass2 - checking and writing primary data (9116 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:42:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.10_summits.bed INFO @ Sun, 21 Jun 2020 20:43:27: Done! pass1 - making usageList (194 chroms): 1 millis pass2 - checking and writing primary data (6007 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:43:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981685/SRX3981685.20_summits.bed INFO @ Sun, 21 Jun 2020 20:43:58: Done! pass1 - making usageList (113 chroms): 1 millis pass2 - checking and writing primary data (2481 records, 4 fields): 7 millis CompletedMACS2peakCalling