Job ID = 6498670 SRX = SRX685462 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:52:21 prefetch.2.10.7: 1) Downloading 'SRR1556384'... 2020-06-25T23:52:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:55:59 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:55:59 prefetch.2.10.7: 1) 'SRR1556384' was downloaded successfully Read 46345316 spots for SRR1556384/SRR1556384.sra Written 46345316 spots for SRR1556384/SRR1556384.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: 00:00:01 Multiseed full-index search: 00:18:36 46345316 reads; of these: 46345316 (100.00%) were unpaired; of these: 1846813 (3.98%) aligned 0 times 28454121 (61.40%) aligned exactly 1 time 16044382 (34.62%) aligned >1 times 96.02% overall alignment rate Time searching: 00:18:37 Overall time: 00:18:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 13868289 / 44498503 = 0.3117 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 @ Fri, 26 Jun 2020 09:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.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 @ Fri, 26 Jun 2020 09:26:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:12: 1000000 INFO @ Fri, 26 Jun 2020 09:26:18: 2000000 INFO @ Fri, 26 Jun 2020 09:26:24: 3000000 INFO @ Fri, 26 Jun 2020 09:26:30: 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 @ Fri, 26 Jun 2020 09:26:35: 5000000 INFO @ Fri, 26 Jun 2020 09:26:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.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 @ Fri, 26 Jun 2020 09:26:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:41: 6000000 INFO @ Fri, 26 Jun 2020 09:26:43: 1000000 INFO @ Fri, 26 Jun 2020 09:26:48: 7000000 INFO @ Fri, 26 Jun 2020 09:26:49: 2000000 INFO @ Fri, 26 Jun 2020 09:26:54: 8000000 INFO @ Fri, 26 Jun 2020 09:26:56: 3000000 INFO @ Fri, 26 Jun 2020 09:27:00: 9000000 INFO @ Fri, 26 Jun 2020 09:27:02: 4000000 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 @ Fri, 26 Jun 2020 09:27:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.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 @ Fri, 26 Jun 2020 09:27:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:27:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:27:06: 10000000 INFO @ Fri, 26 Jun 2020 09:27:08: 5000000 INFO @ Fri, 26 Jun 2020 09:27:13: 11000000 INFO @ Fri, 26 Jun 2020 09:27:13: 1000000 INFO @ Fri, 26 Jun 2020 09:27:14: 6000000 INFO @ Fri, 26 Jun 2020 09:27:19: 2000000 INFO @ Fri, 26 Jun 2020 09:27:19: 12000000 INFO @ Fri, 26 Jun 2020 09:27:21: 7000000 INFO @ Fri, 26 Jun 2020 09:27:26: 3000000 INFO @ Fri, 26 Jun 2020 09:27:26: 13000000 INFO @ Fri, 26 Jun 2020 09:27:27: 8000000 INFO @ Fri, 26 Jun 2020 09:27:32: 4000000 INFO @ Fri, 26 Jun 2020 09:27:33: 14000000 INFO @ Fri, 26 Jun 2020 09:27:34: 9000000 INFO @ Fri, 26 Jun 2020 09:27:39: 5000000 INFO @ Fri, 26 Jun 2020 09:27:39: 15000000 INFO @ Fri, 26 Jun 2020 09:27:40: 10000000 INFO @ Fri, 26 Jun 2020 09:27:45: 6000000 INFO @ Fri, 26 Jun 2020 09:27:46: 16000000 INFO @ Fri, 26 Jun 2020 09:27:47: 11000000 INFO @ Fri, 26 Jun 2020 09:27:52: 7000000 INFO @ Fri, 26 Jun 2020 09:27:52: 17000000 INFO @ Fri, 26 Jun 2020 09:27:53: 12000000 INFO @ Fri, 26 Jun 2020 09:27:58: 8000000 INFO @ Fri, 26 Jun 2020 09:27:59: 18000000 INFO @ Fri, 26 Jun 2020 09:28:00: 13000000 INFO @ Fri, 26 Jun 2020 09:28:05: 9000000 INFO @ Fri, 26 Jun 2020 09:28:06: 19000000 INFO @ Fri, 26 Jun 2020 09:28:06: 14000000 INFO @ Fri, 26 Jun 2020 09:28:11: 10000000 INFO @ Fri, 26 Jun 2020 09:28:12: 20000000 INFO @ Fri, 26 Jun 2020 09:28:13: 15000000 INFO @ Fri, 26 Jun 2020 09:28:17: 11000000 INFO @ Fri, 26 Jun 2020 09:28:19: 21000000 INFO @ Fri, 26 Jun 2020 09:28:20: 16000000 INFO @ Fri, 26 Jun 2020 09:28:24: 12000000 INFO @ Fri, 26 Jun 2020 09:28:25: 22000000 INFO @ Fri, 26 Jun 2020 09:28:26: 17000000 INFO @ Fri, 26 Jun 2020 09:28:31: 13000000 INFO @ Fri, 26 Jun 2020 09:28:32: 23000000 INFO @ Fri, 26 Jun 2020 09:28:33: 18000000 INFO @ Fri, 26 Jun 2020 09:28:37: 14000000 INFO @ Fri, 26 Jun 2020 09:28:39: 24000000 INFO @ Fri, 26 Jun 2020 09:28:39: 19000000 INFO @ Fri, 26 Jun 2020 09:28:44: 15000000 INFO @ Fri, 26 Jun 2020 09:28:45: 25000000 INFO @ Fri, 26 Jun 2020 09:28:46: 20000000 INFO @ Fri, 26 Jun 2020 09:28:50: 16000000 INFO @ Fri, 26 Jun 2020 09:28:52: 26000000 INFO @ Fri, 26 Jun 2020 09:28:53: 21000000 INFO @ Fri, 26 Jun 2020 09:28:57: 17000000 INFO @ Fri, 26 Jun 2020 09:28:58: 27000000 INFO @ Fri, 26 Jun 2020 09:28:59: 22000000 INFO @ Fri, 26 Jun 2020 09:29:04: 18000000 INFO @ Fri, 26 Jun 2020 09:29:05: 28000000 INFO @ Fri, 26 Jun 2020 09:29:06: 23000000 INFO @ Fri, 26 Jun 2020 09:29:10: 19000000 INFO @ Fri, 26 Jun 2020 09:29:12: 29000000 INFO @ Fri, 26 Jun 2020 09:29:13: 24000000 INFO @ Fri, 26 Jun 2020 09:29:17: 20000000 INFO @ Fri, 26 Jun 2020 09:29:18: 30000000 INFO @ Fri, 26 Jun 2020 09:29:19: 25000000 INFO @ Fri, 26 Jun 2020 09:29:23: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:29:23: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:29:23: #1 total tags in treatment: 30630214 INFO @ Fri, 26 Jun 2020 09:29:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:29:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:29:23: #1 tags after filtering in treatment: 30630214 INFO @ Fri, 26 Jun 2020 09:29:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:29:23: #1 finished! INFO @ Fri, 26 Jun 2020 09:29:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:29:24: 21000000 INFO @ Fri, 26 Jun 2020 09:29:25: #2 number of paired peaks: 339 WARNING @ Fri, 26 Jun 2020 09:29:25: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 26 Jun 2020 09:29:25: start model_add_line... INFO @ Fri, 26 Jun 2020 09:29:26: start X-correlation... INFO @ Fri, 26 Jun 2020 09:29:26: end of X-cor INFO @ Fri, 26 Jun 2020 09:29:26: #2 finished! INFO @ Fri, 26 Jun 2020 09:29:26: #2 predicted fragment length is 150 bps INFO @ Fri, 26 Jun 2020 09:29:26: #2 alternative fragment length(s) may be 4,150 bps INFO @ Fri, 26 Jun 2020 09:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.05_model.r INFO @ Fri, 26 Jun 2020 09:29:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:29:26: 26000000 INFO @ Fri, 26 Jun 2020 09:29:30: 22000000 INFO @ Fri, 26 Jun 2020 09:29:32: 27000000 INFO @ Fri, 26 Jun 2020 09:29:37: 23000000 INFO @ Fri, 26 Jun 2020 09:29:39: 28000000 INFO @ Fri, 26 Jun 2020 09:29:44: 24000000 INFO @ Fri, 26 Jun 2020 09:29:46: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:29:51: 25000000 INFO @ Fri, 26 Jun 2020 09:29:53: 30000000 INFO @ Fri, 26 Jun 2020 09:29:57: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:29:57: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:29:57: #1 total tags in treatment: 30630214 INFO @ Fri, 26 Jun 2020 09:29:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:29:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:29:58: 26000000 INFO @ Fri, 26 Jun 2020 09:29:58: #1 tags after filtering in treatment: 30630214 INFO @ Fri, 26 Jun 2020 09:29:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:29:58: #1 finished! INFO @ Fri, 26 Jun 2020 09:29:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:29:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:30:00: #2 number of paired peaks: 339 WARNING @ Fri, 26 Jun 2020 09:30:00: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 26 Jun 2020 09:30:00: start model_add_line... INFO @ Fri, 26 Jun 2020 09:30:00: start X-correlation... INFO @ Fri, 26 Jun 2020 09:30:00: end of X-cor INFO @ Fri, 26 Jun 2020 09:30:00: #2 finished! INFO @ Fri, 26 Jun 2020 09:30:00: #2 predicted fragment length is 150 bps INFO @ Fri, 26 Jun 2020 09:30:00: #2 alternative fragment length(s) may be 4,150 bps INFO @ Fri, 26 Jun 2020 09:30:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.10_model.r INFO @ Fri, 26 Jun 2020 09:30:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:30:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:30:04: 27000000 INFO @ Fri, 26 Jun 2020 09:30:10: 28000000 INFO @ Fri, 26 Jun 2020 09:30:16: 29000000 INFO @ Fri, 26 Jun 2020 09:30:22: 30000000 INFO @ Fri, 26 Jun 2020 09:30:27: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:30:27: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:30:27: #1 total tags in treatment: 30630214 INFO @ Fri, 26 Jun 2020 09:30:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:30:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:30:27: #1 tags after filtering in treatment: 30630214 INFO @ Fri, 26 Jun 2020 09:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:30:27: #1 finished! INFO @ Fri, 26 Jun 2020 09:30:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:30:29: #2 number of paired peaks: 339 WARNING @ Fri, 26 Jun 2020 09:30:29: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 26 Jun 2020 09:30:29: start model_add_line... INFO @ Fri, 26 Jun 2020 09:30:29: start X-correlation... INFO @ Fri, 26 Jun 2020 09:30:29: end of X-cor INFO @ Fri, 26 Jun 2020 09:30:29: #2 finished! INFO @ Fri, 26 Jun 2020 09:30:29: #2 predicted fragment length is 150 bps INFO @ Fri, 26 Jun 2020 09:30:29: #2 alternative fragment length(s) may be 4,150 bps INFO @ Fri, 26 Jun 2020 09:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.20_model.r INFO @ Fri, 26 Jun 2020 09:30:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:30:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:31:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:31:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:31:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.05_summits.bed INFO @ Fri, 26 Jun 2020 09:31:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10083 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:31:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:31:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:31:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:31:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.10_summits.bed INFO @ Fri, 26 Jun 2020 09:31:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6590 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:31:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685462/SRX685462.20_summits.bed INFO @ Fri, 26 Jun 2020 09:32:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3291 records, 4 fields): 5 millis CompletedMACS2peakCalling