Job ID = 6457263 SRX = SRX4639143 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:40:55 prefetch.2.10.7: 1) Downloading 'SRR7784124'... 2020-06-21T11:40:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:45:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:45:54 prefetch.2.10.7: 1) 'SRR7784124' was downloaded successfully Read 31504881 spots for SRR7784124/SRR7784124.sra Written 31504881 spots for SRR7784124/SRR7784124.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:55 31504881 reads; of these: 31504881 (100.00%) were unpaired; of these: 8868240 (28.15%) aligned 0 times 16801957 (53.33%) aligned exactly 1 time 5834684 (18.52%) aligned >1 times 71.85% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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_sort_core] merging from 12 files... [bam_rmdupse_core] 8245653 / 22636641 = 0.3643 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 20:59:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.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 20:59:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:59:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:59:41: 1000000 INFO @ Sun, 21 Jun 2020 20:59:47: 2000000 INFO @ Sun, 21 Jun 2020 20:59:52: 3000000 INFO @ Sun, 21 Jun 2020 20:59:58: 4000000 INFO @ Sun, 21 Jun 2020 21:00:03: 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 21:00:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.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 21:00:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:00:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:00:09: 6000000 INFO @ Sun, 21 Jun 2020 21:00:12: 1000000 INFO @ Sun, 21 Jun 2020 21:00:14: 7000000 INFO @ Sun, 21 Jun 2020 21:00:18: 2000000 INFO @ Sun, 21 Jun 2020 21:00:20: 8000000 INFO @ Sun, 21 Jun 2020 21:00:24: 3000000 INFO @ Sun, 21 Jun 2020 21:00:26: 9000000 INFO @ Sun, 21 Jun 2020 21:00:30: 4000000 INFO @ Sun, 21 Jun 2020 21:00:32: 10000000 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 21:00:36: 5000000 INFO @ Sun, 21 Jun 2020 21:00:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.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 21:00:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:00:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:00:38: 11000000 INFO @ Sun, 21 Jun 2020 21:00:42: 6000000 INFO @ Sun, 21 Jun 2020 21:00:42: 1000000 INFO @ Sun, 21 Jun 2020 21:00:44: 12000000 INFO @ Sun, 21 Jun 2020 21:00:48: 7000000 INFO @ Sun, 21 Jun 2020 21:00:48: 2000000 INFO @ Sun, 21 Jun 2020 21:00:50: 13000000 INFO @ Sun, 21 Jun 2020 21:00:54: 8000000 INFO @ Sun, 21 Jun 2020 21:00:55: 3000000 INFO @ Sun, 21 Jun 2020 21:00:56: 14000000 INFO @ Sun, 21 Jun 2020 21:00:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:00:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:00:59: #1 total tags in treatment: 14390988 INFO @ Sun, 21 Jun 2020 21:00:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:00:59: #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 21:00:59: #1 tags after filtering in treatment: 14390957 INFO @ Sun, 21 Jun 2020 21:00:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:00:59: #1 finished! INFO @ Sun, 21 Jun 2020 21:00:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:01:00: 9000000 INFO @ Sun, 21 Jun 2020 21:01:00: #2 number of paired peaks: 1340 INFO @ Sun, 21 Jun 2020 21:01:00: start model_add_line... INFO @ Sun, 21 Jun 2020 21:01:00: start X-correlation... INFO @ Sun, 21 Jun 2020 21:01:00: end of X-cor INFO @ Sun, 21 Jun 2020 21:01:00: #2 finished! INFO @ Sun, 21 Jun 2020 21:01:00: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:01:00: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.05_model.r INFO @ Sun, 21 Jun 2020 21:01:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:01:01: 4000000 INFO @ Sun, 21 Jun 2020 21:01:06: 10000000 INFO @ Sun, 21 Jun 2020 21:01:07: 5000000 INFO @ Sun, 21 Jun 2020 21:01:12: 11000000 INFO @ Sun, 21 Jun 2020 21:01:13: 6000000 INFO @ Sun, 21 Jun 2020 21:01:18: 12000000 INFO @ Sun, 21 Jun 2020 21:01:19: 7000000 INFO @ Sun, 21 Jun 2020 21:01:25: 13000000 INFO @ Sun, 21 Jun 2020 21:01:26: 8000000 INFO @ Sun, 21 Jun 2020 21:01:31: 14000000 INFO @ Sun, 21 Jun 2020 21:01:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:01:32: 9000000 INFO @ Sun, 21 Jun 2020 21:01:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:01:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:01:33: #1 total tags in treatment: 14390988 INFO @ Sun, 21 Jun 2020 21:01:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:01:33: #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 21:01:34: #1 tags after filtering in treatment: 14390957 INFO @ Sun, 21 Jun 2020 21:01:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:01:34: #1 finished! INFO @ Sun, 21 Jun 2020 21:01:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:01:35: #2 number of paired peaks: 1340 INFO @ Sun, 21 Jun 2020 21:01:35: start model_add_line... INFO @ Sun, 21 Jun 2020 21:01:35: start X-correlation... INFO @ Sun, 21 Jun 2020 21:01:35: end of X-cor INFO @ Sun, 21 Jun 2020 21:01:35: #2 finished! INFO @ Sun, 21 Jun 2020 21:01:35: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:01:35: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:01:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.10_model.r INFO @ Sun, 21 Jun 2020 21:01:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:01:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:01:38: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:01:44: 11000000 INFO @ Sun, 21 Jun 2020 21:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:01:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.05_summits.bed INFO @ Sun, 21 Jun 2020 21:01:47: Done! pass1 - making usageList (726 chroms): 1 millis pass2 - checking and writing primary data (4988 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:01:50: 12000000 INFO @ Sun, 21 Jun 2020 21:01:56: 13000000 INFO @ Sun, 21 Jun 2020 21:02:01: 14000000 INFO @ Sun, 21 Jun 2020 21:02:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:02:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:02:04: #1 total tags in treatment: 14390988 INFO @ Sun, 21 Jun 2020 21:02:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:04: #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 21:02:04: #1 tags after filtering in treatment: 14390957 INFO @ Sun, 21 Jun 2020 21:02:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:02:05: #2 number of paired peaks: 1340 INFO @ Sun, 21 Jun 2020 21:02:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:05: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:02:05: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:02:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.20_model.r INFO @ Sun, 21 Jun 2020 21:02:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:02:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:02:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:02:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.10_summits.bed INFO @ Sun, 21 Jun 2020 21:02:19: Done! pass1 - making usageList (625 chroms): 1 millis pass2 - checking and writing primary data (3232 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:02:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:02:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:02:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:02:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639143/SRX4639143.20_summits.bed INFO @ Sun, 21 Jun 2020 21:02:50: Done! pass1 - making usageList (554 chroms): 1 millis pass2 - checking and writing primary data (2130 records, 4 fields): 17 millis CompletedMACS2peakCalling