Job ID = 6366661 SRX = SRX216762 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:46:14 prefetch.2.10.7: 1) Downloading 'SRR648396'... 2020-06-15T23:46:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:14 prefetch.2.10.7: 1) 'SRR648396' was downloaded successfully Read 28546628 spots for SRR648396/SRR648396.sra Written 28546628 spots for SRR648396/SRR648396.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: 00:06:06 28546628 reads; of these: 28546628 (100.00%) were unpaired; of these: 3925691 (13.75%) aligned 0 times 21691228 (75.99%) aligned exactly 1 time 2929709 (10.26%) aligned >1 times 86.25% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5921382 / 24620937 = 0.2405 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 @ Tue, 16 Jun 2020 09:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:06:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:40: 1000000 INFO @ Tue, 16 Jun 2020 09:06:49: 2000000 INFO @ Tue, 16 Jun 2020 09:06:57: 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 @ Tue, 16 Jun 2020 09:07:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:07:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:05: 4000000 INFO @ Tue, 16 Jun 2020 09:07:11: 1000000 INFO @ Tue, 16 Jun 2020 09:07:13: 5000000 INFO @ Tue, 16 Jun 2020 09:07:20: 2000000 INFO @ Tue, 16 Jun 2020 09:07:21: 6000000 INFO @ Tue, 16 Jun 2020 09:07:29: 3000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 09:07:29: 7000000 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 @ Tue, 16 Jun 2020 09:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:07:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:38: 8000000 INFO @ Tue, 16 Jun 2020 09:07:38: 4000000 INFO @ Tue, 16 Jun 2020 09:07:41: 1000000 INFO @ Tue, 16 Jun 2020 09:07:46: 9000000 INFO @ Tue, 16 Jun 2020 09:07:47: 5000000 INFO @ Tue, 16 Jun 2020 09:07:50: 2000000 INFO @ Tue, 16 Jun 2020 09:07:55: 10000000 INFO @ Tue, 16 Jun 2020 09:07:57: 6000000 INFO @ Tue, 16 Jun 2020 09:07:59: 3000000 INFO @ Tue, 16 Jun 2020 09:08:03: 11000000 INFO @ Tue, 16 Jun 2020 09:08:06: 7000000 INFO @ Tue, 16 Jun 2020 09:08:09: 4000000 INFO @ Tue, 16 Jun 2020 09:08:12: 12000000 INFO @ Tue, 16 Jun 2020 09:08:15: 8000000 INFO @ Tue, 16 Jun 2020 09:08:18: 5000000 INFO @ Tue, 16 Jun 2020 09:08:20: 13000000 INFO @ Tue, 16 Jun 2020 09:08:24: 9000000 INFO @ Tue, 16 Jun 2020 09:08:27: 6000000 INFO @ Tue, 16 Jun 2020 09:08:27: 14000000 INFO @ Tue, 16 Jun 2020 09:08:33: 10000000 INFO @ Tue, 16 Jun 2020 09:08:36: 7000000 INFO @ Tue, 16 Jun 2020 09:08:36: 15000000 INFO @ Tue, 16 Jun 2020 09:08:43: 11000000 INFO @ Tue, 16 Jun 2020 09:08:43: 16000000 INFO @ Tue, 16 Jun 2020 09:08:45: 8000000 INFO @ Tue, 16 Jun 2020 09:08:50: 17000000 INFO @ Tue, 16 Jun 2020 09:08:52: 12000000 INFO @ Tue, 16 Jun 2020 09:08:54: 9000000 INFO @ Tue, 16 Jun 2020 09:08:57: 18000000 INFO @ Tue, 16 Jun 2020 09:09:01: 13000000 INFO @ Tue, 16 Jun 2020 09:09:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:09:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:09:03: #1 total tags in treatment: 18699555 INFO @ Tue, 16 Jun 2020 09:09:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:09:03: #1 tags after filtering in treatment: 18699555 INFO @ Tue, 16 Jun 2020 09:09:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:03: 10000000 INFO @ Tue, 16 Jun 2020 09:09:04: #2 number of paired peaks: 204 WARNING @ Tue, 16 Jun 2020 09:09:04: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:05: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:09:05: #2 alternative fragment length(s) may be 3,118 bps INFO @ Tue, 16 Jun 2020 09:09:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.05_model.r INFO @ Tue, 16 Jun 2020 09:09:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:11: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:09:13: 11000000 INFO @ Tue, 16 Jun 2020 09:09:20: 15000000 INFO @ Tue, 16 Jun 2020 09:09:22: 12000000 INFO @ Tue, 16 Jun 2020 09:09:30: 16000000 INFO @ Tue, 16 Jun 2020 09:09:32: 13000000 INFO @ Tue, 16 Jun 2020 09:09:39: 17000000 INFO @ Tue, 16 Jun 2020 09:09:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:41: 14000000 INFO @ Tue, 16 Jun 2020 09:09:48: 18000000 INFO @ Tue, 16 Jun 2020 09:09:50: 15000000 INFO @ Tue, 16 Jun 2020 09:09:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:09:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:09:55: #1 total tags in treatment: 18699555 INFO @ Tue, 16 Jun 2020 09:09:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:09:55: #1 tags after filtering in treatment: 18699555 INFO @ Tue, 16 Jun 2020 09:09:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:56: #2 number of paired peaks: 204 WARNING @ Tue, 16 Jun 2020 09:09:56: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:56: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:09:56: #2 alternative fragment length(s) may be 3,118 bps INFO @ Tue, 16 Jun 2020 09:09:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.10_model.r INFO @ Tue, 16 Jun 2020 09:09:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.05_summits.bed INFO @ Tue, 16 Jun 2020 09:09:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4054 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:00: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:10:09: 17000000 INFO @ Tue, 16 Jun 2020 09:10:19: 18000000 INFO @ Tue, 16 Jun 2020 09:10:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:10:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:10:25: #1 total tags in treatment: 18699555 INFO @ Tue, 16 Jun 2020 09:10:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:10:25: #1 tags after filtering in treatment: 18699555 INFO @ Tue, 16 Jun 2020 09:10:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:27: #2 number of paired peaks: 204 WARNING @ Tue, 16 Jun 2020 09:10:27: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:27: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:10:27: #2 alternative fragment length(s) may be 3,118 bps INFO @ Tue, 16 Jun 2020 09:10:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.20_model.r INFO @ Tue, 16 Jun 2020 09:10:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.10_summits.bed INFO @ Tue, 16 Jun 2020 09:10:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2155 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216762/SRX216762.20_summits.bed INFO @ Tue, 16 Jun 2020 09:11:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (783 records, 4 fields): 3 millis CompletedMACS2peakCalling