Job ID = 6454917 SRX = SRX2592499 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:43:25 prefetch.2.10.7: 1) Downloading 'SRR5289776'... 2020-06-21T09:43:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:34 prefetch.2.10.7: 1) 'SRR5289776' was downloaded successfully Read 19055976 spots for SRR5289776/SRR5289776.sra Written 19055976 spots for SRR5289776/SRR5289776.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: 00:03:42 19055976 reads; of these: 19055976 (100.00%) were unpaired; of these: 4730361 (24.82%) aligned 0 times 12698619 (66.64%) aligned exactly 1 time 1626996 (8.54%) aligned >1 times 75.18% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 3557964 / 14325615 = 0.2484 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 18:55:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.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 18:55:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:10: 1000000 INFO @ Sun, 21 Jun 2020 18:55:16: 2000000 INFO @ Sun, 21 Jun 2020 18:55:22: 3000000 INFO @ Sun, 21 Jun 2020 18:55:28: 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 18:55:34: 5000000 INFO @ Sun, 21 Jun 2020 18:55:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.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 18:55:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:40: 6000000 INFO @ Sun, 21 Jun 2020 18:55:41: 1000000 INFO @ Sun, 21 Jun 2020 18:55:47: 7000000 INFO @ Sun, 21 Jun 2020 18:55:48: 2000000 INFO @ Sun, 21 Jun 2020 18:55:54: 8000000 INFO @ Sun, 21 Jun 2020 18:55:55: 3000000 INFO @ Sun, 21 Jun 2020 18:56:01: 9000000 INFO @ Sun, 21 Jun 2020 18:56:02: 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 @ Sun, 21 Jun 2020 18:56:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.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 18:56:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:08: 10000000 INFO @ Sun, 21 Jun 2020 18:56:08: 5000000 INFO @ Sun, 21 Jun 2020 18:56:11: 1000000 INFO @ Sun, 21 Jun 2020 18:56:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:56:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:56:13: #1 total tags in treatment: 10767651 INFO @ Sun, 21 Jun 2020 18:56:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:13: #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 18:56:13: #1 tags after filtering in treatment: 10767468 INFO @ Sun, 21 Jun 2020 18:56:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:15: #2 number of paired peaks: 9194 INFO @ Sun, 21 Jun 2020 18:56:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:15: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 18:56:15: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 18:56:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.05_model.r INFO @ Sun, 21 Jun 2020 18:56:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:15: 6000000 INFO @ Sun, 21 Jun 2020 18:56:18: 2000000 INFO @ Sun, 21 Jun 2020 18:56:22: 7000000 INFO @ Sun, 21 Jun 2020 18:56:25: 3000000 INFO @ Sun, 21 Jun 2020 18:56:28: 8000000 INFO @ Sun, 21 Jun 2020 18:56:31: 4000000 INFO @ Sun, 21 Jun 2020 18:56:36: 9000000 INFO @ Sun, 21 Jun 2020 18:56:38: 5000000 INFO @ Sun, 21 Jun 2020 18:56:42: 10000000 INFO @ Sun, 21 Jun 2020 18:56:45: 6000000 INFO @ Sun, 21 Jun 2020 18:56:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:56:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:56:48: #1 total tags in treatment: 10767651 INFO @ Sun, 21 Jun 2020 18:56:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:48: #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 18:56:48: #1 tags after filtering in treatment: 10767468 INFO @ Sun, 21 Jun 2020 18:56:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:48: #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 18:56:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:56:49: #2 number of paired peaks: 9194 INFO @ Sun, 21 Jun 2020 18:56:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:49: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 18:56:49: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 18:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.10_model.r INFO @ Sun, 21 Jun 2020 18:56:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:51: 7000000 INFO @ Sun, 21 Jun 2020 18:56:57: 8000000 INFO @ Sun, 21 Jun 2020 18:57:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.05_summits.bed INFO @ Sun, 21 Jun 2020 18:57:04: Done! INFO @ Sun, 21 Jun 2020 18:57:04: 9000000 pass1 - making usageList (95 chroms): 2 millis pass2 - checking and writing primary data (11384 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:57:10: 10000000 INFO @ Sun, 21 Jun 2020 18:57:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:57:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:57:15: #1 total tags in treatment: 10767651 INFO @ Sun, 21 Jun 2020 18:57:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:15: #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 18:57:15: #1 tags after filtering in treatment: 10767468 INFO @ Sun, 21 Jun 2020 18:57:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:16: #2 number of paired peaks: 9194 INFO @ Sun, 21 Jun 2020 18:57:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:17: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 18:57:17: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 18:57:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.20_model.r INFO @ Sun, 21 Jun 2020 18:57:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.10_summits.bed INFO @ Sun, 21 Jun 2020 18:57:39: Done! pass1 - making usageList (76 chroms): 2 millis pass2 - checking and writing primary data (9143 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592499/SRX2592499.20_summits.bed INFO @ Sun, 21 Jun 2020 18:58:06: Done! pass1 - making usageList (43 chroms): 2 millis pass2 - checking and writing primary data (6748 records, 4 fields): 9 millis CompletedMACS2peakCalling