Job ID = 6452649 SRX = SRX022745 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:52:15 prefetch.2.10.7: 1) Downloading 'SRR059124'... 2020-06-21T07:52:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:52:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:52:57 prefetch.2.10.7: 'SRR059124' is valid 2020-06-21T07:52:57 prefetch.2.10.7: 1) 'SRR059124' was downloaded successfully Read 9739953 spots for SRR059124/SRR059124.sra Written 9739953 spots for SRR059124/SRR059124.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: 00:01:56 9739953 reads; of these: 9739953 (100.00%) were unpaired; of these: 986171 (10.13%) aligned 0 times 7018563 (72.06%) aligned exactly 1 time 1735219 (17.82%) aligned >1 times 89.87% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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_rmdupse_core] 1083206 / 8753782 = 0.1237 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 16:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.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 16:57:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:34: 1000000 INFO @ Sun, 21 Jun 2020 16:57:39: 2000000 INFO @ Sun, 21 Jun 2020 16:57:43: 3000000 INFO @ Sun, 21 Jun 2020 16:57:48: 4000000 INFO @ Sun, 21 Jun 2020 16:57:53: 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 16:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.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 16:57:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:58: 6000000 INFO @ Sun, 21 Jun 2020 16:58:04: 1000000 INFO @ Sun, 21 Jun 2020 16:58:04: 7000000 INFO @ Sun, 21 Jun 2020 16:58:08: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:08: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:08: #1 total tags in treatment: 7670576 INFO @ Sun, 21 Jun 2020 16:58:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:08: #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 16:58:08: #1 tags after filtering in treatment: 7670451 INFO @ Sun, 21 Jun 2020 16:58:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:08: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:09: 2000000 INFO @ Sun, 21 Jun 2020 16:58:09: #2 number of paired peaks: 2916 INFO @ Sun, 21 Jun 2020 16:58:09: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:09: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:09: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:09: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:09: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 16:58:09: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 16:58:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.05_model.r INFO @ Sun, 21 Jun 2020 16:58:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:58:14: 3000000 INFO @ Sun, 21 Jun 2020 16:58:19: 4000000 INFO @ Sun, 21 Jun 2020 16:58:24: 5000000 INFO @ Sun, 21 Jun 2020 16:58:25: #3 Call peaks for each chromosome... 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 16:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.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 16:58:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:58:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:29: 6000000 INFO @ Sun, 21 Jun 2020 16:58:34: 1000000 INFO @ Sun, 21 Jun 2020 16:58:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.05_summits.bed INFO @ Sun, 21 Jun 2020 16:58:34: Done! pass1 - making usageList (249 chroms): 3 millis pass2 - checking and writing primary data (7377 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:58:35: 7000000 INFO @ Sun, 21 Jun 2020 16:58:39: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:39: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:39: #1 total tags in treatment: 7670576 INFO @ Sun, 21 Jun 2020 16:58:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:39: #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 16:58:39: #1 tags after filtering in treatment: 7670451 INFO @ Sun, 21 Jun 2020 16:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:39: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:39: 2000000 INFO @ Sun, 21 Jun 2020 16:58:40: #2 number of paired peaks: 2916 INFO @ Sun, 21 Jun 2020 16:58:40: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:40: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:40: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:40: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:40: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 16:58:40: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 16:58:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.10_model.r INFO @ Sun, 21 Jun 2020 16:58:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:58:44: 3000000 INFO @ Sun, 21 Jun 2020 16:58:50: 4000000 INFO @ Sun, 21 Jun 2020 16:58:55: 5000000 INFO @ Sun, 21 Jun 2020 16:58:56: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:59:00: 6000000 INFO @ Sun, 21 Jun 2020 16:59:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.10_summits.bed INFO @ Sun, 21 Jun 2020 16:59:05: Done! pass1 - making usageList (173 chroms): 1 millis pass2 - checking and writing primary data (5179 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:59:06: 7000000 INFO @ Sun, 21 Jun 2020 16:59:09: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:59:09: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:59:09: #1 total tags in treatment: 7670576 INFO @ Sun, 21 Jun 2020 16:59:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:59:09: #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 16:59:09: #1 tags after filtering in treatment: 7670451 INFO @ Sun, 21 Jun 2020 16:59:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:59:09: #1 finished! INFO @ Sun, 21 Jun 2020 16:59:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:59:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:59:10: #2 number of paired peaks: 2916 INFO @ Sun, 21 Jun 2020 16:59:10: start model_add_line... INFO @ Sun, 21 Jun 2020 16:59:10: start X-correlation... INFO @ Sun, 21 Jun 2020 16:59:10: end of X-cor INFO @ Sun, 21 Jun 2020 16:59:10: #2 finished! INFO @ Sun, 21 Jun 2020 16:59:10: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 16:59:10: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 16:59:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.20_model.r INFO @ Sun, 21 Jun 2020 16:59:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:59:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:59:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:59:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022745/SRX022745.20_summits.bed INFO @ Sun, 21 Jun 2020 16:59:35: Done! pass1 - making usageList (141 chroms): 2 millis pass2 - checking and writing primary data (3322 records, 4 fields): 8 millis CompletedMACS2peakCalling