Job ID = 6456657 SRX = SRX3909719 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:16:54 prefetch.2.10.7: 1) Downloading 'SRR6967846'... 2020-06-21T11:16:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:35 prefetch.2.10.7: 1) 'SRR6967846' was downloaded successfully Read 26155350 spots for SRR6967846/SRR6967846.sra Written 26155350 spots for SRR6967846/SRR6967846.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: 00:06:00 26155350 reads; of these: 26155350 (100.00%) were unpaired; of these: 3766874 (14.40%) aligned 0 times 17977042 (68.73%) aligned exactly 1 time 4411434 (16.87%) aligned >1 times 85.60% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 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] 4523981 / 22388476 = 0.2021 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 20:35:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.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 20:35:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:35:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:35:19: 1000000 INFO @ Sun, 21 Jun 2020 20:35:25: 2000000 INFO @ Sun, 21 Jun 2020 20:35:31: 3000000 INFO @ Sun, 21 Jun 2020 20:35:37: 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 20:35:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.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 20:35:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:35:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:35:44: 5000000 INFO @ Sun, 21 Jun 2020 20:35:51: 1000000 INFO @ Sun, 21 Jun 2020 20:35:51: 6000000 INFO @ Sun, 21 Jun 2020 20:35:59: 7000000 INFO @ Sun, 21 Jun 2020 20:35:59: 2000000 INFO @ Sun, 21 Jun 2020 20:36:06: 8000000 INFO @ Sun, 21 Jun 2020 20:36:07: 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 20:36:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.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 20:36:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:36:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:36:14: 9000000 INFO @ Sun, 21 Jun 2020 20:36:15: 4000000 INFO @ Sun, 21 Jun 2020 20:36:21: 1000000 INFO @ Sun, 21 Jun 2020 20:36:22: 10000000 INFO @ Sun, 21 Jun 2020 20:36:23: 5000000 INFO @ Sun, 21 Jun 2020 20:36:29: 2000000 INFO @ Sun, 21 Jun 2020 20:36:29: 11000000 INFO @ Sun, 21 Jun 2020 20:36:31: 6000000 INFO @ Sun, 21 Jun 2020 20:36:36: 3000000 INFO @ Sun, 21 Jun 2020 20:36:37: 12000000 INFO @ Sun, 21 Jun 2020 20:36:39: 7000000 INFO @ Sun, 21 Jun 2020 20:36:44: 4000000 INFO @ Sun, 21 Jun 2020 20:36:45: 13000000 INFO @ Sun, 21 Jun 2020 20:36:48: 8000000 INFO @ Sun, 21 Jun 2020 20:36:52: 5000000 INFO @ Sun, 21 Jun 2020 20:36:53: 14000000 INFO @ Sun, 21 Jun 2020 20:36:56: 9000000 INFO @ Sun, 21 Jun 2020 20:37:00: 6000000 INFO @ Sun, 21 Jun 2020 20:37:01: 15000000 INFO @ Sun, 21 Jun 2020 20:37:04: 10000000 INFO @ Sun, 21 Jun 2020 20:37:08: 7000000 INFO @ Sun, 21 Jun 2020 20:37:08: 16000000 INFO @ Sun, 21 Jun 2020 20:37:12: 11000000 INFO @ Sun, 21 Jun 2020 20:37:16: 8000000 INFO @ Sun, 21 Jun 2020 20:37:16: 17000000 INFO @ Sun, 21 Jun 2020 20:37:21: 12000000 INFO @ Sun, 21 Jun 2020 20:37:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:37:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:37:23: #1 total tags in treatment: 17864495 INFO @ Sun, 21 Jun 2020 20:37:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:37:23: #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 20:37:23: 9000000 INFO @ Sun, 21 Jun 2020 20:37:24: #1 tags after filtering in treatment: 17864484 INFO @ Sun, 21 Jun 2020 20:37:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:37:24: #1 finished! INFO @ Sun, 21 Jun 2020 20:37:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:37:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:37:25: #2 number of paired peaks: 1242 INFO @ Sun, 21 Jun 2020 20:37:25: start model_add_line... INFO @ Sun, 21 Jun 2020 20:37:25: start X-correlation... INFO @ Sun, 21 Jun 2020 20:37:25: end of X-cor INFO @ Sun, 21 Jun 2020 20:37:25: #2 finished! INFO @ Sun, 21 Jun 2020 20:37:25: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 20:37:25: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 20:37:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.05_model.r INFO @ Sun, 21 Jun 2020 20:37:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:37:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:37:29: 13000000 INFO @ Sun, 21 Jun 2020 20:37:31: 10000000 INFO @ Sun, 21 Jun 2020 20:37:37: 14000000 INFO @ Sun, 21 Jun 2020 20:37:39: 11000000 INFO @ Sun, 21 Jun 2020 20:37:45: 15000000 INFO @ Sun, 21 Jun 2020 20:37:47: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:37:54: 16000000 INFO @ Sun, 21 Jun 2020 20:37:54: 13000000 INFO @ Sun, 21 Jun 2020 20:38:02: 17000000 INFO @ Sun, 21 Jun 2020 20:38:02: 14000000 INFO @ Sun, 21 Jun 2020 20:38:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:38:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:38:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:38:09: #1 total tags in treatment: 17864495 INFO @ Sun, 21 Jun 2020 20:38:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:38:09: #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 20:38:10: #1 tags after filtering in treatment: 17864484 INFO @ Sun, 21 Jun 2020 20:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:38:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:38:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:38:10: 15000000 INFO @ Sun, 21 Jun 2020 20:38:11: #2 number of paired peaks: 1242 INFO @ Sun, 21 Jun 2020 20:38:11: start model_add_line... INFO @ Sun, 21 Jun 2020 20:38:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:38:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:38:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:38:11: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 20:38:11: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 20:38:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.10_model.r INFO @ Sun, 21 Jun 2020 20:38:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:38:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:38:17: 16000000 INFO @ Sun, 21 Jun 2020 20:38:23: 17000000 INFO @ Sun, 21 Jun 2020 20:38:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.05_summits.bed INFO @ Sun, 21 Jun 2020 20:38:23: Done! pass1 - making usageList (569 chroms): 2 millis pass2 - checking and writing primary data (9560 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:38:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:38:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:38:29: #1 total tags in treatment: 17864495 INFO @ Sun, 21 Jun 2020 20:38:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:38:29: #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 20:38:29: #1 tags after filtering in treatment: 17864484 INFO @ Sun, 21 Jun 2020 20:38:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:38:29: #1 finished! INFO @ Sun, 21 Jun 2020 20:38:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:38:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:38:31: #2 number of paired peaks: 1242 INFO @ Sun, 21 Jun 2020 20:38:31: start model_add_line... INFO @ Sun, 21 Jun 2020 20:38:31: start X-correlation... INFO @ Sun, 21 Jun 2020 20:38:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:38:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:38:31: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 20:38:31: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 20:38:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.20_model.r INFO @ Sun, 21 Jun 2020 20:38:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:38:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:38:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:39:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:39:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:39:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.10_summits.bed INFO @ Sun, 21 Jun 2020 20:39:05: Done! pass1 - making usageList (491 chroms): 2 millis pass2 - checking and writing primary data (6413 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:39:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:39:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:39:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:39:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3909719/SRX3909719.20_summits.bed INFO @ Sun, 21 Jun 2020 20:39:29: Done! pass1 - making usageList (286 chroms): 1 millis pass2 - checking and writing primary data (3543 records, 4 fields): 13 millis CompletedMACS2peakCalling