Job ID = 6457118 SRX = SRX4451934 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:41:28 prefetch.2.10.7: 1) Downloading 'SRR7586078'... 2020-06-21T11:41:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:45:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:45:53 prefetch.2.10.7: 1) 'SRR7586078' was downloaded successfully 2020-06-21T11:45:53 prefetch.2.10.7: 'SRR7586078' has 0 unresolved dependencies Read 25512165 spots for SRR7586078/SRR7586078.sra Written 25512165 spots for SRR7586078/SRR7586078.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: 00:06:58 25512165 reads; of these: 25512165 (100.00%) were unpaired; of these: 8532830 (33.45%) aligned 0 times 14423731 (56.54%) aligned exactly 1 time 2555604 (10.02%) aligned >1 times 66.55% overall alignment rate Time searching: 00:06:58 Overall time: 00:06:58 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] 4868379 / 16979335 = 0.2867 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 21:00:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.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 21:00:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:00:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:00:39: 1000000 INFO @ Sun, 21 Jun 2020 21:00:47: 2000000 INFO @ Sun, 21 Jun 2020 21:00:54: 3000000 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 21:01:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.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 21:01:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:01:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:01:02: 4000000 INFO @ Sun, 21 Jun 2020 21:01:09: 1000000 INFO @ Sun, 21 Jun 2020 21:01:09: 5000000 INFO @ Sun, 21 Jun 2020 21:01:17: 2000000 INFO @ Sun, 21 Jun 2020 21:01:17: 6000000 INFO @ Sun, 21 Jun 2020 21:01:25: 7000000 INFO @ Sun, 21 Jun 2020 21:01:25: 3000000 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 21:01:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.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 21:01:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:01:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:01:32: 4000000 INFO @ Sun, 21 Jun 2020 21:01:32: 8000000 INFO @ Sun, 21 Jun 2020 21:01:37: 1000000 INFO @ Sun, 21 Jun 2020 21:01:40: 5000000 INFO @ Sun, 21 Jun 2020 21:01:40: 9000000 INFO @ Sun, 21 Jun 2020 21:01:44: 2000000 INFO @ Sun, 21 Jun 2020 21:01:47: 6000000 INFO @ Sun, 21 Jun 2020 21:01:48: 10000000 INFO @ Sun, 21 Jun 2020 21:01:49: 3000000 INFO @ Sun, 21 Jun 2020 21:01:55: 7000000 INFO @ Sun, 21 Jun 2020 21:01:55: 4000000 INFO @ Sun, 21 Jun 2020 21:01:56: 11000000 INFO @ Sun, 21 Jun 2020 21:02:01: 5000000 INFO @ Sun, 21 Jun 2020 21:02:02: 8000000 INFO @ Sun, 21 Jun 2020 21:02:04: 12000000 INFO @ Sun, 21 Jun 2020 21:02:05: #1 tag size is determined as 79 bps INFO @ Sun, 21 Jun 2020 21:02:05: #1 tag size = 79 INFO @ Sun, 21 Jun 2020 21:02:05: #1 total tags in treatment: 12110956 INFO @ Sun, 21 Jun 2020 21:02:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:05: #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 21:02:06: #1 tags after filtering in treatment: 12110794 INFO @ Sun, 21 Jun 2020 21:02:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:06: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:07: #2 number of paired peaks: 1183 INFO @ Sun, 21 Jun 2020 21:02:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:07: #2 predicted fragment length is 195 bps INFO @ Sun, 21 Jun 2020 21:02:07: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 21 Jun 2020 21:02:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.05_model.r INFO @ Sun, 21 Jun 2020 21:02:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:07: 6000000 INFO @ Sun, 21 Jun 2020 21:02:10: 9000000 INFO @ Sun, 21 Jun 2020 21:02:13: 7000000 INFO @ Sun, 21 Jun 2020 21:02:18: 10000000 INFO @ Sun, 21 Jun 2020 21:02:19: 8000000 INFO @ Sun, 21 Jun 2020 21:02:25: 9000000 INFO @ Sun, 21 Jun 2020 21:02:26: 11000000 INFO @ Sun, 21 Jun 2020 21:02:32: 10000000 INFO @ Sun, 21 Jun 2020 21:02:34: 12000000 INFO @ Sun, 21 Jun 2020 21:02:35: #1 tag size is determined as 79 bps INFO @ Sun, 21 Jun 2020 21:02:35: #1 tag size = 79 INFO @ Sun, 21 Jun 2020 21:02:35: #1 total tags in treatment: 12110956 INFO @ Sun, 21 Jun 2020 21:02:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:35: #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 21:02:36: #1 tags after filtering in treatment: 12110794 INFO @ Sun, 21 Jun 2020 21:02:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:37: #2 number of paired peaks: 1183 INFO @ Sun, 21 Jun 2020 21:02:37: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:37: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:37: #2 predicted fragment length is 195 bps INFO @ Sun, 21 Jun 2020 21:02:37: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 21 Jun 2020 21:02:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.10_model.r INFO @ Sun, 21 Jun 2020 21:02:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:02:37: 11000000 INFO @ Sun, 21 Jun 2020 21:02:43: 12000000 INFO @ Sun, 21 Jun 2020 21:02:44: #1 tag size is determined as 79 bps INFO @ Sun, 21 Jun 2020 21:02:44: #1 tag size = 79 INFO @ Sun, 21 Jun 2020 21:02:44: #1 total tags in treatment: 12110956 INFO @ Sun, 21 Jun 2020 21:02:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:02:45: #1 tags after filtering in treatment: 12110794 INFO @ Sun, 21 Jun 2020 21:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:46: #2 number of paired peaks: 1183 INFO @ Sun, 21 Jun 2020 21:02:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:46: #2 predicted fragment length is 195 bps INFO @ Sun, 21 Jun 2020 21:02:46: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 21 Jun 2020 21:02:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.20_model.r INFO @ Sun, 21 Jun 2020 21:02:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:02:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:02:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.05_summits.bed INFO @ Sun, 21 Jun 2020 21:02:51: Done! pass1 - making usageList (265 chroms): 2 millis pass2 - checking and writing primary data (5050 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:03:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:03:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:03:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:03:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:03:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.10_summits.bed INFO @ Sun, 21 Jun 2020 21:03:20: Done! pass1 - making usageList (167 chroms): 2 millis pass2 - checking and writing primary data (3767 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:03:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:03:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:03:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4451934/SRX4451934.20_summits.bed INFO @ Sun, 21 Jun 2020 21:03:26: Done! pass1 - making usageList (99 chroms): 2 millis pass2 - checking and writing primary data (2619 records, 4 fields): 24 millis CompletedMACS2peakCalling