Job ID = 6454843 SRX = SRX2592438 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:21:29 prefetch.2.10.7: 1) Downloading 'SRR5289715'... 2020-06-21T09:21:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:23:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:23:56 prefetch.2.10.7: 'SRR5289715' is valid 2020-06-21T09:23:56 prefetch.2.10.7: 1) 'SRR5289715' was downloaded successfully Read 12734283 spots for SRR5289715/SRR5289715.sra Written 12734283 spots for SRR5289715/SRR5289715.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: 00:03:47 12734283 reads; of these: 12734283 (100.00%) were unpaired; of these: 1196720 (9.40%) aligned 0 times 9743462 (76.51%) aligned exactly 1 time 1794101 (14.09%) aligned >1 times 90.60% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 2408979 / 11537563 = 0.2088 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 18:32:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.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 18:32:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:04: 1000000 INFO @ Sun, 21 Jun 2020 18:33:10: 2000000 INFO @ Sun, 21 Jun 2020 18:33:15: 3000000 INFO @ Sun, 21 Jun 2020 18:33:20: 4000000 INFO @ Sun, 21 Jun 2020 18:33:25: 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 18:33:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.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 18:33:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:30: 6000000 INFO @ Sun, 21 Jun 2020 18:33:35: 1000000 INFO @ Sun, 21 Jun 2020 18:33:36: 7000000 INFO @ Sun, 21 Jun 2020 18:33:40: 2000000 INFO @ Sun, 21 Jun 2020 18:33:41: 8000000 INFO @ Sun, 21 Jun 2020 18:33:46: 3000000 INFO @ Sun, 21 Jun 2020 18:33:47: 9000000 INFO @ Sun, 21 Jun 2020 18:33:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:33:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:33:48: #1 total tags in treatment: 9128584 INFO @ Sun, 21 Jun 2020 18:33:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:48: #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 18:33:48: #1 tags after filtering in treatment: 9128419 INFO @ Sun, 21 Jun 2020 18:33:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:49: #2 number of paired peaks: 1646 INFO @ Sun, 21 Jun 2020 18:33:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:49: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 18:33:49: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 18:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.05_model.r INFO @ Sun, 21 Jun 2020 18:33:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:51: 4000000 INFO @ Sun, 21 Jun 2020 18:33:56: 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 18:33:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.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 18:33:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:01: 6000000 INFO @ Sun, 21 Jun 2020 18:34:04: 1000000 INFO @ Sun, 21 Jun 2020 18:34:07: 7000000 INFO @ Sun, 21 Jun 2020 18:34:09: 2000000 INFO @ Sun, 21 Jun 2020 18:34:12: 8000000 INFO @ Sun, 21 Jun 2020 18:34:14: 3000000 INFO @ Sun, 21 Jun 2020 18:34:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:17: 9000000 INFO @ Sun, 21 Jun 2020 18:34:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:34:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:34:18: #1 total tags in treatment: 9128584 INFO @ Sun, 21 Jun 2020 18:34:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:18: #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 18:34:18: #1 tags after filtering in treatment: 9128419 INFO @ Sun, 21 Jun 2020 18:34:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:19: 4000000 INFO @ Sun, 21 Jun 2020 18:34:19: #2 number of paired peaks: 1646 INFO @ Sun, 21 Jun 2020 18:34:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:19: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 18:34:19: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 18:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.10_model.r INFO @ Sun, 21 Jun 2020 18:34:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:24: 5000000 INFO @ Sun, 21 Jun 2020 18:34:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.05_summits.bed INFO @ Sun, 21 Jun 2020 18:34:26: Done! pass1 - making usageList (308 chroms): 3 millis pass2 - checking and writing primary data (16725 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:29: 6000000 INFO @ Sun, 21 Jun 2020 18:34:35: 7000000 INFO @ Sun, 21 Jun 2020 18:34:40: 8000000 INFO @ Sun, 21 Jun 2020 18:34:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:45: 9000000 INFO @ Sun, 21 Jun 2020 18:34:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:34:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:34:46: #1 total tags in treatment: 9128584 INFO @ Sun, 21 Jun 2020 18:34:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:46: #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 18:34:47: #1 tags after filtering in treatment: 9128419 INFO @ Sun, 21 Jun 2020 18:34:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:47: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:34:48: #2 number of paired peaks: 1646 INFO @ Sun, 21 Jun 2020 18:34:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:48: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 18:34:48: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 18:34:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.20_model.r INFO @ Sun, 21 Jun 2020 18:34:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.10_summits.bed INFO @ Sun, 21 Jun 2020 18:34:55: Done! pass1 - making usageList (256 chroms): 3 millis pass2 - checking and writing primary data (10889 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:35:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592438/SRX2592438.20_summits.bed INFO @ Sun, 21 Jun 2020 18:35:23: Done! pass1 - making usageList (196 chroms): 2 millis pass2 - checking and writing primary data (4994 records, 4 fields): 17 millis CompletedMACS2peakCalling