Job ID = 6453577 SRX = SRX127437 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:29:41 prefetch.2.10.7: 1) Downloading 'SRR438684'... 2020-06-21T08:29:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:35:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:35:39 prefetch.2.10.7: 1) 'SRR438684' was downloaded successfully Read 31535696 spots for SRR438684/SRR438684.sra Written 31535696 spots for SRR438684/SRR438684.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: 00:05:31 31535696 reads; of these: 31535696 (100.00%) were unpaired; of these: 6936307 (22.00%) aligned 0 times 20605293 (65.34%) aligned exactly 1 time 3994096 (12.67%) aligned >1 times 78.00% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 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 8 files... [bam_rmdupse_core] 7641480 / 24599389 = 0.3106 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 17:47:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.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 17:47:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:54: 1000000 INFO @ Sun, 21 Jun 2020 17:48:00: 2000000 INFO @ Sun, 21 Jun 2020 17:48:07: 3000000 INFO @ Sun, 21 Jun 2020 17:48:13: 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 17:48:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.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 17:48:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:19: 5000000 INFO @ Sun, 21 Jun 2020 17:48:24: 1000000 INFO @ Sun, 21 Jun 2020 17:48:26: 6000000 INFO @ Sun, 21 Jun 2020 17:48:30: 2000000 INFO @ Sun, 21 Jun 2020 17:48:32: 7000000 INFO @ Sun, 21 Jun 2020 17:48:36: 3000000 INFO @ Sun, 21 Jun 2020 17:48:39: 8000000 INFO @ Sun, 21 Jun 2020 17:48:41: 4000000 INFO @ Sun, 21 Jun 2020 17:48:46: 9000000 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 17:48:47: 5000000 INFO @ Sun, 21 Jun 2020 17:48:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.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 17:48:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:52: 10000000 INFO @ Sun, 21 Jun 2020 17:48:53: 6000000 INFO @ Sun, 21 Jun 2020 17:48:54: 1000000 INFO @ Sun, 21 Jun 2020 17:48:59: 11000000 INFO @ Sun, 21 Jun 2020 17:48:59: 7000000 INFO @ Sun, 21 Jun 2020 17:49:00: 2000000 INFO @ Sun, 21 Jun 2020 17:49:05: 8000000 INFO @ Sun, 21 Jun 2020 17:49:06: 12000000 INFO @ Sun, 21 Jun 2020 17:49:06: 3000000 INFO @ Sun, 21 Jun 2020 17:49:11: 9000000 INFO @ Sun, 21 Jun 2020 17:49:12: 4000000 INFO @ Sun, 21 Jun 2020 17:49:12: 13000000 INFO @ Sun, 21 Jun 2020 17:49:17: 10000000 INFO @ Sun, 21 Jun 2020 17:49:18: 5000000 INFO @ Sun, 21 Jun 2020 17:49:19: 14000000 INFO @ Sun, 21 Jun 2020 17:49:23: 11000000 INFO @ Sun, 21 Jun 2020 17:49:24: 6000000 INFO @ Sun, 21 Jun 2020 17:49:26: 15000000 INFO @ Sun, 21 Jun 2020 17:49:30: 12000000 INFO @ Sun, 21 Jun 2020 17:49:30: 7000000 INFO @ Sun, 21 Jun 2020 17:49:32: 16000000 INFO @ Sun, 21 Jun 2020 17:49:36: 13000000 INFO @ Sun, 21 Jun 2020 17:49:36: 8000000 INFO @ Sun, 21 Jun 2020 17:49:39: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 17:49:39: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 17:49:39: #1 total tags in treatment: 16957909 INFO @ Sun, 21 Jun 2020 17:49:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:39: #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 17:49:40: #1 tags after filtering in treatment: 16957901 INFO @ Sun, 21 Jun 2020 17:49:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:41: #2 number of paired peaks: 4372 INFO @ Sun, 21 Jun 2020 17:49:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:41: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 17:49:41: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 17:49:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.05_model.r INFO @ Sun, 21 Jun 2020 17:49:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:42: 9000000 INFO @ Sun, 21 Jun 2020 17:49:42: 14000000 INFO @ Sun, 21 Jun 2020 17:49:48: 10000000 INFO @ Sun, 21 Jun 2020 17:49:48: 15000000 INFO @ Sun, 21 Jun 2020 17:49:53: 11000000 INFO @ Sun, 21 Jun 2020 17:49:54: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:49:59: 12000000 INFO @ Sun, 21 Jun 2020 17:50:00: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 17:50:00: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 17:50:00: #1 total tags in treatment: 16957909 INFO @ Sun, 21 Jun 2020 17:50:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:00: #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 17:50:00: #1 tags after filtering in treatment: 16957901 INFO @ Sun, 21 Jun 2020 17:50:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:02: #2 number of paired peaks: 4372 INFO @ Sun, 21 Jun 2020 17:50:02: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:02: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:02: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:02: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:02: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 17:50:02: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 17:50:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.10_model.r INFO @ Sun, 21 Jun 2020 17:50:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:05: 13000000 INFO @ Sun, 21 Jun 2020 17:50:10: 14000000 INFO @ Sun, 21 Jun 2020 17:50:16: 15000000 INFO @ Sun, 21 Jun 2020 17:50:21: 16000000 INFO @ Sun, 21 Jun 2020 17:50:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:26: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 17:50:26: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 17:50:26: #1 total tags in treatment: 16957909 INFO @ Sun, 21 Jun 2020 17:50:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:50:27: #1 tags after filtering in treatment: 16957901 INFO @ Sun, 21 Jun 2020 17:50:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:28: #2 number of paired peaks: 4372 INFO @ Sun, 21 Jun 2020 17:50:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:28: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 17:50:28: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 17:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.20_model.r INFO @ Sun, 21 Jun 2020 17:50:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.05_summits.bed INFO @ Sun, 21 Jun 2020 17:50:46: Done! pass1 - making usageList (282 chroms): 3 millis pass2 - checking and writing primary data (9643 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.10_summits.bed INFO @ Sun, 21 Jun 2020 17:51:06: Done! pass1 - making usageList (173 chroms): 1 millis pass2 - checking and writing primary data (6365 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:51:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX127437/SRX127437.20_summits.bed INFO @ Sun, 21 Jun 2020 17:51:32: Done! pass1 - making usageList (105 chroms): 2 millis pass2 - checking and writing primary data (3922 records, 4 fields): 11 millis CompletedMACS2peakCalling