Job ID = 6458881 SRX = SRX5717049 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:51:37 prefetch.2.10.7: 1) Downloading 'SRR8936410'... 2020-06-21T12:51:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:57:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:57:09 prefetch.2.10.7: 1) 'SRR8936410' was downloaded successfully Read 26595355 spots for SRR8936410/SRR8936410.sra Written 26595355 spots for SRR8936410/SRR8936410.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: 00:06:34 26595355 reads; of these: 26595355 (100.00%) were unpaired; of these: 3623409 (13.62%) aligned 0 times 17125590 (64.39%) aligned exactly 1 time 5846356 (21.98%) aligned >1 times 86.38% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 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 12 files... [bam_rmdupse_core] 7618131 / 22971946 = 0.3316 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 22:11:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.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 22:11:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:08: 1000000 INFO @ Sun, 21 Jun 2020 22:11:14: 2000000 INFO @ Sun, 21 Jun 2020 22:11:20: 3000000 INFO @ Sun, 21 Jun 2020 22:11:26: 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 22:11:32: 5000000 INFO @ Sun, 21 Jun 2020 22:11:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.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 22:11:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:38: 6000000 INFO @ Sun, 21 Jun 2020 22:11:39: 1000000 INFO @ Sun, 21 Jun 2020 22:11:44: 7000000 INFO @ Sun, 21 Jun 2020 22:11:46: 2000000 INFO @ Sun, 21 Jun 2020 22:11:50: 8000000 INFO @ Sun, 21 Jun 2020 22:11:53: 3000000 INFO @ Sun, 21 Jun 2020 22:11:56: 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 22:12:00: 4000000 INFO @ Sun, 21 Jun 2020 22:12:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.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 22:12:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:12:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:12:02: 10000000 INFO @ Sun, 21 Jun 2020 22:12:07: 5000000 INFO @ Sun, 21 Jun 2020 22:12:08: 11000000 INFO @ Sun, 21 Jun 2020 22:12:09: 1000000 INFO @ Sun, 21 Jun 2020 22:12:15: 6000000 INFO @ Sun, 21 Jun 2020 22:12:15: 12000000 INFO @ Sun, 21 Jun 2020 22:12:17: 2000000 INFO @ Sun, 21 Jun 2020 22:12:22: 13000000 INFO @ Sun, 21 Jun 2020 22:12:22: 7000000 INFO @ Sun, 21 Jun 2020 22:12:24: 3000000 INFO @ Sun, 21 Jun 2020 22:12:28: 14000000 INFO @ Sun, 21 Jun 2020 22:12:30: 8000000 INFO @ Sun, 21 Jun 2020 22:12:32: 4000000 INFO @ Sun, 21 Jun 2020 22:12:34: 15000000 INFO @ Sun, 21 Jun 2020 22:12:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:12:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:12:37: #1 total tags in treatment: 15353815 INFO @ Sun, 21 Jun 2020 22:12:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:37: #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 22:12:37: 9000000 INFO @ Sun, 21 Jun 2020 22:12:37: #1 tags after filtering in treatment: 15353745 INFO @ Sun, 21 Jun 2020 22:12:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:12:37: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:12:39: #2 number of paired peaks: 1085 INFO @ Sun, 21 Jun 2020 22:12:39: start model_add_line... INFO @ Sun, 21 Jun 2020 22:12:39: start X-correlation... INFO @ Sun, 21 Jun 2020 22:12:39: end of X-cor INFO @ Sun, 21 Jun 2020 22:12:39: #2 finished! INFO @ Sun, 21 Jun 2020 22:12:39: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 22:12:39: #2 alternative fragment length(s) may be 28,107,144,557 bps INFO @ Sun, 21 Jun 2020 22:12:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.05_model.r INFO @ Sun, 21 Jun 2020 22:12:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:12:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:12:39: 5000000 INFO @ Sun, 21 Jun 2020 22:12:45: 10000000 INFO @ Sun, 21 Jun 2020 22:12:47: 6000000 INFO @ Sun, 21 Jun 2020 22:12:52: 11000000 INFO @ Sun, 21 Jun 2020 22:12:55: 7000000 INFO @ Sun, 21 Jun 2020 22:13:00: 12000000 INFO @ Sun, 21 Jun 2020 22:13:02: 8000000 INFO @ Sun, 21 Jun 2020 22:13:07: 13000000 INFO @ Sun, 21 Jun 2020 22:13:08: 9000000 INFO @ Sun, 21 Jun 2020 22:13:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:13:13: 14000000 INFO @ Sun, 21 Jun 2020 22:13:15: 10000000 INFO @ Sun, 21 Jun 2020 22:13:19: 15000000 INFO @ Sun, 21 Jun 2020 22:13:21: 11000000 INFO @ Sun, 21 Jun 2020 22:13:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:13:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:13:22: #1 total tags in treatment: 15353815 INFO @ Sun, 21 Jun 2020 22:13:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:22: #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 22:13:22: #1 tags after filtering in treatment: 15353745 INFO @ Sun, 21 Jun 2020 22:13:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:22: #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 22:13:24: #2 number of paired peaks: 1085 INFO @ Sun, 21 Jun 2020 22:13:24: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:24: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:24: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:24: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:24: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 22:13:24: #2 alternative fragment length(s) may be 28,107,144,557 bps INFO @ Sun, 21 Jun 2020 22:13:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.10_model.r INFO @ Sun, 21 Jun 2020 22:13:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.05_summits.bed INFO @ Sun, 21 Jun 2020 22:13:25: Done! pass1 - making usageList (498 chroms): 2 millis pass2 - checking and writing primary data (2025 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:13:27: 12000000 INFO @ Sun, 21 Jun 2020 22:13:33: 13000000 INFO @ Sun, 21 Jun 2020 22:13:38: 14000000 INFO @ Sun, 21 Jun 2020 22:13:44: 15000000 INFO @ Sun, 21 Jun 2020 22:13:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:13:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:13:46: #1 total tags in treatment: 15353815 INFO @ Sun, 21 Jun 2020 22:13:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:46: #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 22:13:47: #1 tags after filtering in treatment: 15353745 INFO @ Sun, 21 Jun 2020 22:13:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:47: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:48: #2 number of paired peaks: 1085 INFO @ Sun, 21 Jun 2020 22:13:48: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:48: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:48: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:48: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:48: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 22:13:48: #2 alternative fragment length(s) may be 28,107,144,557 bps INFO @ Sun, 21 Jun 2020 22:13:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.20_model.r INFO @ Sun, 21 Jun 2020 22:13:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:14:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.10_summits.bed INFO @ Sun, 21 Jun 2020 22:14:09: Done! pass1 - making usageList (435 chroms): 2 millis pass2 - checking and writing primary data (1061 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:14:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:14:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717049/SRX5717049.20_summits.bed INFO @ Sun, 21 Jun 2020 22:14:33: Done! pass1 - making usageList (293 chroms): 1 millis pass2 - checking and writing primary data (500 records, 4 fields): 16 millis CompletedMACS2peakCalling