Job ID = 6453416 SRX = SRX1134698 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:30:26 prefetch.2.10.7: 1) Downloading 'SRR2147079'... 2020-06-21T08:30:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:23 prefetch.2.10.7: 1) 'SRR2147079' was downloaded successfully 2020-06-21T08:33:23 prefetch.2.10.7: 'SRR2147079' has 0 unresolved dependencies Read 19431754 spots for SRR2147079/SRR2147079.sra Written 19431754 spots for SRR2147079/SRR2147079.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: 00:04:00 19431754 reads; of these: 19431754 (100.00%) were unpaired; of these: 1902723 (9.79%) aligned 0 times 15364954 (79.07%) aligned exactly 1 time 2164077 (11.14%) aligned >1 times 90.21% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 9439531 / 17529031 = 0.5385 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 17:42:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.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 17:42:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:42:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:42:24: 1000000 INFO @ Sun, 21 Jun 2020 17:42:30: 2000000 INFO @ Sun, 21 Jun 2020 17:42:35: 3000000 INFO @ Sun, 21 Jun 2020 17:42:40: 4000000 INFO @ Sun, 21 Jun 2020 17:42:45: 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 17:42:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.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 17:42:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:42:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:42:50: 6000000 INFO @ Sun, 21 Jun 2020 17:42:55: 1000000 INFO @ Sun, 21 Jun 2020 17:42:56: 7000000 INFO @ Sun, 21 Jun 2020 17:43:01: 2000000 INFO @ Sun, 21 Jun 2020 17:43:02: 8000000 INFO @ Sun, 21 Jun 2020 17:43:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:43:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:43:03: #1 total tags in treatment: 8089500 INFO @ Sun, 21 Jun 2020 17:43:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:43:03: #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 17:43:03: #1 tags after filtering in treatment: 8089342 INFO @ Sun, 21 Jun 2020 17:43:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:43:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:43:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:43:04: #2 number of paired peaks: 3656 INFO @ Sun, 21 Jun 2020 17:43:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:43:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:43:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:43:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:43:04: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 17:43:04: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 17:43:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.05_model.r INFO @ Sun, 21 Jun 2020 17:43:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:43:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:43:06: 3000000 INFO @ Sun, 21 Jun 2020 17:43:12: 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 17:43:17: 5000000 INFO @ Sun, 21 Jun 2020 17:43:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.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 17:43:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:43:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:43:23: 6000000 INFO @ Sun, 21 Jun 2020 17:43:25: 1000000 INFO @ Sun, 21 Jun 2020 17:43:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:43:29: 7000000 INFO @ Sun, 21 Jun 2020 17:43:30: 2000000 INFO @ Sun, 21 Jun 2020 17:43:34: 8000000 INFO @ Sun, 21 Jun 2020 17:43:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:43:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:43:35: #1 total tags in treatment: 8089500 INFO @ Sun, 21 Jun 2020 17:43:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:43:35: #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 17:43:35: #1 tags after filtering in treatment: 8089342 INFO @ Sun, 21 Jun 2020 17:43:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:43:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:43:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:43:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:43:36: #2 number of paired peaks: 3656 INFO @ Sun, 21 Jun 2020 17:43:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:43:36: 3000000 INFO @ Sun, 21 Jun 2020 17:43:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:43:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:43:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:43:36: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 17:43:36: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 17:43:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.10_model.r INFO @ Sun, 21 Jun 2020 17:43:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:43:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:43:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:43:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:43:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.05_summits.bed INFO @ Sun, 21 Jun 2020 17:43:38: Done! pass1 - making usageList (119 chroms): 2 millis pass2 - checking and writing primary data (5215 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:43:42: 4000000 INFO @ Sun, 21 Jun 2020 17:43:47: 5000000 INFO @ Sun, 21 Jun 2020 17:43:52: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:43:58: 7000000 INFO @ Sun, 21 Jun 2020 17:44:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:44:03: 8000000 INFO @ Sun, 21 Jun 2020 17:44:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:44:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:44:04: #1 total tags in treatment: 8089500 INFO @ Sun, 21 Jun 2020 17:44:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:44:04: #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 17:44:04: #1 tags after filtering in treatment: 8089342 INFO @ Sun, 21 Jun 2020 17:44:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:44:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:44:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:44:05: #2 number of paired peaks: 3656 INFO @ Sun, 21 Jun 2020 17:44:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:44:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:44:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:44:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:44:05: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 17:44:05: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 17:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.20_model.r INFO @ Sun, 21 Jun 2020 17:44:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:44:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.10_summits.bed INFO @ Sun, 21 Jun 2020 17:44:11: Done! pass1 - making usageList (103 chroms): 1 millis pass2 - checking and writing primary data (3919 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:44:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:44:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:44:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:44:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134698/SRX1134698.20_summits.bed INFO @ Sun, 21 Jun 2020 17:44:38: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (2773 records, 4 fields): 6 millis CompletedMACS2peakCalling