Job ID = 6457081 SRX = SRX4375844 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:52:18 prefetch.2.10.7: 1) Downloading 'SRR7506498'... 2020-06-21T11:52:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:54:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:54:21 prefetch.2.10.7: 1) 'SRR7506498' was downloaded successfully Read 17054008 spots for SRR7506498/SRR7506498.sra Written 17054008 spots for SRR7506498/SRR7506498.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: 00:03:54 17054008 reads; of these: 17054008 (100.00%) were unpaired; of these: 2452300 (14.38%) aligned 0 times 12197602 (71.52%) aligned exactly 1 time 2404106 (14.10%) aligned >1 times 85.62% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 4070141 / 14601708 = 0.2787 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 21:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.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 21:02:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:02:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:03:03: 1000000 INFO @ Sun, 21 Jun 2020 21:03:10: 2000000 INFO @ Sun, 21 Jun 2020 21:03:17: 3000000 INFO @ Sun, 21 Jun 2020 21:03:24: 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 21:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.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 21:03:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:03:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:03:31: 5000000 INFO @ Sun, 21 Jun 2020 21:03:33: 1000000 INFO @ Sun, 21 Jun 2020 21:03:38: 6000000 INFO @ Sun, 21 Jun 2020 21:03:40: 2000000 INFO @ Sun, 21 Jun 2020 21:03:46: 7000000 INFO @ Sun, 21 Jun 2020 21:03:48: 3000000 INFO @ Sun, 21 Jun 2020 21:03:53: 8000000 INFO @ Sun, 21 Jun 2020 21:03:55: 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 21:03:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.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 21:03:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:03:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:04:01: 9000000 INFO @ Sun, 21 Jun 2020 21:04:02: 5000000 INFO @ Sun, 21 Jun 2020 21:04:04: 1000000 INFO @ Sun, 21 Jun 2020 21:04:08: 10000000 INFO @ Sun, 21 Jun 2020 21:04:10: 6000000 INFO @ Sun, 21 Jun 2020 21:04:12: 2000000 INFO @ Sun, 21 Jun 2020 21:04:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:04:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:04:12: #1 total tags in treatment: 10531567 INFO @ Sun, 21 Jun 2020 21:04:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:04:12: #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 21:04:13: #1 tags after filtering in treatment: 10531364 INFO @ Sun, 21 Jun 2020 21:04:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:04:13: #1 finished! INFO @ Sun, 21 Jun 2020 21:04:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:04:14: #2 number of paired peaks: 7855 INFO @ Sun, 21 Jun 2020 21:04:14: start model_add_line... INFO @ Sun, 21 Jun 2020 21:04:14: start X-correlation... INFO @ Sun, 21 Jun 2020 21:04:14: end of X-cor INFO @ Sun, 21 Jun 2020 21:04:14: #2 finished! INFO @ Sun, 21 Jun 2020 21:04:14: #2 predicted fragment length is 197 bps INFO @ Sun, 21 Jun 2020 21:04:14: #2 alternative fragment length(s) may be 197 bps INFO @ Sun, 21 Jun 2020 21:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.05_model.r INFO @ Sun, 21 Jun 2020 21:04:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:04:16: 7000000 INFO @ Sun, 21 Jun 2020 21:04:18: 3000000 INFO @ Sun, 21 Jun 2020 21:04:22: 8000000 INFO @ Sun, 21 Jun 2020 21:04:24: 4000000 INFO @ Sun, 21 Jun 2020 21:04:29: 9000000 INFO @ Sun, 21 Jun 2020 21:04:30: 5000000 INFO @ Sun, 21 Jun 2020 21:04:34: 10000000 INFO @ Sun, 21 Jun 2020 21:04:36: 6000000 INFO @ Sun, 21 Jun 2020 21:04:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:04:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:04:38: #1 total tags in treatment: 10531567 INFO @ Sun, 21 Jun 2020 21:04:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:04:38: #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 21:04:38: #1 tags after filtering in treatment: 10531364 INFO @ Sun, 21 Jun 2020 21:04:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:04:38: #1 finished! INFO @ Sun, 21 Jun 2020 21:04:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:04:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:04:39: #2 number of paired peaks: 7855 INFO @ Sun, 21 Jun 2020 21:04:39: start model_add_line... INFO @ Sun, 21 Jun 2020 21:04:39: start X-correlation... INFO @ Sun, 21 Jun 2020 21:04:39: end of X-cor INFO @ Sun, 21 Jun 2020 21:04:39: #2 finished! INFO @ Sun, 21 Jun 2020 21:04:39: #2 predicted fragment length is 197 bps INFO @ Sun, 21 Jun 2020 21:04:39: #2 alternative fragment length(s) may be 197 bps INFO @ Sun, 21 Jun 2020 21:04:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.10_model.r INFO @ Sun, 21 Jun 2020 21:04:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:04:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:04:41: 7000000 INFO @ Sun, 21 Jun 2020 21:04:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:04:47: 8000000 INFO @ Sun, 21 Jun 2020 21:04:53: 9000000 INFO @ Sun, 21 Jun 2020 21:04:59: 10000000 INFO @ Sun, 21 Jun 2020 21:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.05_summits.bed INFO @ Sun, 21 Jun 2020 21:04:59: Done! pass1 - making usageList (173 chroms): 2 millis pass2 - checking and writing primary data (10017 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:05:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:05:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:05:02: #1 total tags in treatment: 10531567 INFO @ Sun, 21 Jun 2020 21:05:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:05:02: #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 21:05:02: #1 tags after filtering in treatment: 10531364 INFO @ Sun, 21 Jun 2020 21:05:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:05:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:05:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:05:03: #2 number of paired peaks: 7855 INFO @ Sun, 21 Jun 2020 21:05:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:05:04: start X-correlation... INFO @ Sun, 21 Jun 2020 21:05:04: end of X-cor INFO @ Sun, 21 Jun 2020 21:05:04: #2 finished! INFO @ Sun, 21 Jun 2020 21:05:04: #2 predicted fragment length is 197 bps INFO @ Sun, 21 Jun 2020 21:05:04: #2 alternative fragment length(s) may be 197 bps INFO @ Sun, 21 Jun 2020 21:05:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.20_model.r INFO @ Sun, 21 Jun 2020 21:05:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:05:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:05:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:05:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:05:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:05:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.10_summits.bed INFO @ Sun, 21 Jun 2020 21:05:25: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (7528 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:05:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:05:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:05:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:05:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375844/SRX4375844.20_summits.bed INFO @ Sun, 21 Jun 2020 21:05:50: Done! pass1 - making usageList (95 chroms): 2 millis pass2 - checking and writing primary data (5304 records, 4 fields): 9 millis CompletedMACS2peakCalling