Job ID = 6454960 SRX = SRX2618503 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:34:55 prefetch.2.10.7: 1) Downloading 'SRR5319057'... 2020-06-21T09:34:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:40:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:40:07 prefetch.2.10.7: 1) 'SRR5319057' was downloaded successfully 2020-06-21T09:40:07 prefetch.2.10.7: 'SRR5319057' has 0 unresolved dependencies Read 43517163 spots for SRR5319057/SRR5319057.sra Written 43517163 spots for SRR5319057/SRR5319057.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: 00:08:35 43517163 reads; of these: 43517163 (100.00%) were unpaired; of these: 11738390 (26.97%) aligned 0 times 28499158 (65.49%) aligned exactly 1 time 3279615 (7.54%) aligned >1 times 73.03% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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 16 files... [bam_rmdupse_core] 5225212 / 31778773 = 0.1644 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 18:58:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.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 18:58:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:13: 1000000 INFO @ Sun, 21 Jun 2020 18:58:20: 2000000 INFO @ Sun, 21 Jun 2020 18:58:27: 3000000 INFO @ Sun, 21 Jun 2020 18:58:34: 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 18:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.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 18:58:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:41: 5000000 INFO @ Sun, 21 Jun 2020 18:58:44: 1000000 INFO @ Sun, 21 Jun 2020 18:58:48: 6000000 INFO @ Sun, 21 Jun 2020 18:58:52: 2000000 INFO @ Sun, 21 Jun 2020 18:58:56: 7000000 INFO @ Sun, 21 Jun 2020 18:59:00: 3000000 INFO @ Sun, 21 Jun 2020 18:59:04: 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 18:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.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 18:59:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:08: 4000000 INFO @ Sun, 21 Jun 2020 18:59:12: 9000000 INFO @ Sun, 21 Jun 2020 18:59:15: 1000000 INFO @ Sun, 21 Jun 2020 18:59:16: 5000000 INFO @ Sun, 21 Jun 2020 18:59:20: 10000000 INFO @ Sun, 21 Jun 2020 18:59:23: 2000000 INFO @ Sun, 21 Jun 2020 18:59:24: 6000000 INFO @ Sun, 21 Jun 2020 18:59:28: 11000000 INFO @ Sun, 21 Jun 2020 18:59:32: 3000000 INFO @ Sun, 21 Jun 2020 18:59:33: 7000000 INFO @ Sun, 21 Jun 2020 18:59:35: 12000000 INFO @ Sun, 21 Jun 2020 18:59:40: 4000000 INFO @ Sun, 21 Jun 2020 18:59:41: 8000000 INFO @ Sun, 21 Jun 2020 18:59:43: 13000000 INFO @ Sun, 21 Jun 2020 18:59:47: 5000000 INFO @ Sun, 21 Jun 2020 18:59:49: 9000000 INFO @ Sun, 21 Jun 2020 18:59:51: 14000000 INFO @ Sun, 21 Jun 2020 18:59:55: 6000000 INFO @ Sun, 21 Jun 2020 18:59:57: 10000000 INFO @ Sun, 21 Jun 2020 18:59:59: 15000000 INFO @ Sun, 21 Jun 2020 19:00:02: 7000000 INFO @ Sun, 21 Jun 2020 19:00:05: 11000000 INFO @ Sun, 21 Jun 2020 19:00:07: 16000000 INFO @ Sun, 21 Jun 2020 19:00:11: 8000000 INFO @ Sun, 21 Jun 2020 19:00:13: 12000000 INFO @ Sun, 21 Jun 2020 19:00:15: 17000000 INFO @ Sun, 21 Jun 2020 19:00:18: 9000000 INFO @ Sun, 21 Jun 2020 19:00:21: 13000000 INFO @ Sun, 21 Jun 2020 19:00:23: 18000000 INFO @ Sun, 21 Jun 2020 19:00:26: 10000000 INFO @ Sun, 21 Jun 2020 19:00:29: 14000000 INFO @ Sun, 21 Jun 2020 19:00:32: 19000000 INFO @ Sun, 21 Jun 2020 19:00:34: 11000000 INFO @ Sun, 21 Jun 2020 19:00:37: 15000000 INFO @ Sun, 21 Jun 2020 19:00:40: 20000000 INFO @ Sun, 21 Jun 2020 19:00:42: 12000000 INFO @ Sun, 21 Jun 2020 19:00:45: 16000000 INFO @ Sun, 21 Jun 2020 19:00:48: 21000000 INFO @ Sun, 21 Jun 2020 19:00:50: 13000000 INFO @ Sun, 21 Jun 2020 19:00:54: 17000000 INFO @ Sun, 21 Jun 2020 19:00:57: 22000000 INFO @ Sun, 21 Jun 2020 19:00:58: 14000000 INFO @ Sun, 21 Jun 2020 19:01:02: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:01:05: 23000000 INFO @ Sun, 21 Jun 2020 19:01:06: 15000000 INFO @ Sun, 21 Jun 2020 19:01:10: 19000000 INFO @ Sun, 21 Jun 2020 19:01:13: 24000000 INFO @ Sun, 21 Jun 2020 19:01:14: 16000000 INFO @ Sun, 21 Jun 2020 19:01:18: 20000000 INFO @ Sun, 21 Jun 2020 19:01:21: 25000000 INFO @ Sun, 21 Jun 2020 19:01:21: 17000000 INFO @ Sun, 21 Jun 2020 19:01:26: 21000000 INFO @ Sun, 21 Jun 2020 19:01:29: 26000000 INFO @ Sun, 21 Jun 2020 19:01:29: 18000000 INFO @ Sun, 21 Jun 2020 19:01:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:01:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:01:33: #1 total tags in treatment: 26553561 INFO @ Sun, 21 Jun 2020 19:01:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:33: #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 19:01:34: 22000000 INFO @ Sun, 21 Jun 2020 19:01:34: #1 tags after filtering in treatment: 26553557 INFO @ Sun, 21 Jun 2020 19:01:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:34: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:36: #2 number of paired peaks: 450 WARNING @ Sun, 21 Jun 2020 19:01:36: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Sun, 21 Jun 2020 19:01:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:36: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 19:01:36: #2 alternative fragment length(s) may be 3,142,155 bps INFO @ Sun, 21 Jun 2020 19:01:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.05_model.r INFO @ Sun, 21 Jun 2020 19:01:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:37: 19000000 INFO @ Sun, 21 Jun 2020 19:01:41: 23000000 INFO @ Sun, 21 Jun 2020 19:01:44: 20000000 INFO @ Sun, 21 Jun 2020 19:01:49: 24000000 INFO @ Sun, 21 Jun 2020 19:01:52: 21000000 INFO @ Sun, 21 Jun 2020 19:01:56: 25000000 INFO @ Sun, 21 Jun 2020 19:01:59: 22000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:02:04: 26000000 INFO @ Sun, 21 Jun 2020 19:02:07: 23000000 INFO @ Sun, 21 Jun 2020 19:02:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:08: #1 total tags in treatment: 26553561 INFO @ Sun, 21 Jun 2020 19:02:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:08: #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 19:02:09: #1 tags after filtering in treatment: 26553557 INFO @ Sun, 21 Jun 2020 19:02:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:09: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:11: #2 number of paired peaks: 450 WARNING @ Sun, 21 Jun 2020 19:02:11: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Sun, 21 Jun 2020 19:02:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:11: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 19:02:11: #2 alternative fragment length(s) may be 3,142,155 bps INFO @ Sun, 21 Jun 2020 19:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.10_model.r INFO @ Sun, 21 Jun 2020 19:02:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:14: 24000000 INFO @ Sun, 21 Jun 2020 19:02:20: 25000000 INFO @ Sun, 21 Jun 2020 19:02:27: 26000000 INFO @ Sun, 21 Jun 2020 19:02:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:31: #1 total tags in treatment: 26553561 INFO @ Sun, 21 Jun 2020 19:02:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:31: #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 19:02:32: #1 tags after filtering in treatment: 26553557 INFO @ Sun, 21 Jun 2020 19:02:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:34: #2 number of paired peaks: 450 WARNING @ Sun, 21 Jun 2020 19:02:34: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Sun, 21 Jun 2020 19:02:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:34: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 19:02:34: #2 alternative fragment length(s) may be 3,142,155 bps INFO @ Sun, 21 Jun 2020 19:02:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.20_model.r INFO @ Sun, 21 Jun 2020 19:02:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.05_summits.bed INFO @ Sun, 21 Jun 2020 19:03:02: Done! pass1 - making usageList (382 chroms): 2 millis pass2 - checking and writing primary data (10308 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.10_summits.bed INFO @ Sun, 21 Jun 2020 19:03:39: Done! pass1 - making usageList (262 chroms): 2 millis pass2 - checking and writing primary data (6190 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618503/SRX2618503.20_summits.bed INFO @ Sun, 21 Jun 2020 19:03:58: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (2168 records, 4 fields): 7 millis CompletedMACS2peakCalling