Job ID = 6366692 SRX = SRX2228848 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:52:03 prefetch.2.10.7: 1) Downloading 'SRR4380304'... 2020-06-15T23:52:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:31 prefetch.2.10.7: 1) 'SRR4380304' was downloaded successfully Read 23585231 spots for SRR4380304/SRR4380304.sra Written 23585231 spots for SRR4380304/SRR4380304.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: 00:03:59 23585231 reads; of these: 23585231 (100.00%) were unpaired; of these: 2089418 (8.86%) aligned 0 times 18033956 (76.46%) aligned exactly 1 time 3461857 (14.68%) aligned >1 times 91.14% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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 8 files... [bam_rmdupse_core] 11682802 / 21495813 = 0.5435 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 09:05:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.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 09:05:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:23: 1000000 INFO @ Tue, 16 Jun 2020 09:05:30: 2000000 INFO @ Tue, 16 Jun 2020 09:05:37: 3000000 INFO @ Tue, 16 Jun 2020 09:05:44: 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 @ Tue, 16 Jun 2020 09:05:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.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 09:05:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:51: 5000000 INFO @ Tue, 16 Jun 2020 09:05:55: 1000000 INFO @ Tue, 16 Jun 2020 09:05:58: 6000000 INFO @ Tue, 16 Jun 2020 09:06:02: 2000000 INFO @ Tue, 16 Jun 2020 09:06:04: 7000000 INFO @ Tue, 16 Jun 2020 09:06:10: 3000000 INFO @ Tue, 16 Jun 2020 09:06:10: 8000000 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 @ Tue, 16 Jun 2020 09:06:17: 4000000 INFO @ Tue, 16 Jun 2020 09:06:17: 9000000 INFO @ Tue, 16 Jun 2020 09:06:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.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 09:06:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:22: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:06:22: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:06:22: #1 total tags in treatment: 9813011 INFO @ Tue, 16 Jun 2020 09:06:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:22: #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 09:06:23: #1 tags after filtering in treatment: 9813011 INFO @ Tue, 16 Jun 2020 09:06:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:23: #2 number of paired peaks: 682 WARNING @ Tue, 16 Jun 2020 09:06:23: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Tue, 16 Jun 2020 09:06:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:23: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:06:23: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 16 Jun 2020 09:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.05_model.r INFO @ Tue, 16 Jun 2020 09:06:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:06:24: 5000000 INFO @ Tue, 16 Jun 2020 09:06:24: 1000000 INFO @ Tue, 16 Jun 2020 09:06:30: 2000000 INFO @ Tue, 16 Jun 2020 09:06:31: 6000000 INFO @ Tue, 16 Jun 2020 09:06:36: 3000000 INFO @ Tue, 16 Jun 2020 09:06:38: 7000000 INFO @ Tue, 16 Jun 2020 09:06:43: 4000000 INFO @ Tue, 16 Jun 2020 09:06:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:46: 8000000 INFO @ Tue, 16 Jun 2020 09:06:49: 5000000 INFO @ Tue, 16 Jun 2020 09:06:53: 9000000 INFO @ Tue, 16 Jun 2020 09:06:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.05_summits.bed INFO @ Tue, 16 Jun 2020 09:06:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2885 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:06:55: 6000000 INFO @ Tue, 16 Jun 2020 09:06:58: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:06:58: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:06:58: #1 total tags in treatment: 9813011 INFO @ Tue, 16 Jun 2020 09:06:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:58: #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 09:06:59: #1 tags after filtering in treatment: 9813011 INFO @ Tue, 16 Jun 2020 09:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:59: #2 number of paired peaks: 682 WARNING @ Tue, 16 Jun 2020 09:06:59: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Tue, 16 Jun 2020 09:06:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:59: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:06:59: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 16 Jun 2020 09:06:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.10_model.r INFO @ Tue, 16 Jun 2020 09:06:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:01: 7000000 INFO @ Tue, 16 Jun 2020 09:07:07: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:07:13: 9000000 INFO @ Tue, 16 Jun 2020 09:07:18: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:07:18: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:07:18: #1 total tags in treatment: 9813011 INFO @ Tue, 16 Jun 2020 09:07:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:18: #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 09:07:18: #1 tags after filtering in treatment: 9813011 INFO @ Tue, 16 Jun 2020 09:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:19: #2 number of paired peaks: 682 WARNING @ Tue, 16 Jun 2020 09:07:19: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:19: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:07:19: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 16 Jun 2020 09:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.20_model.r INFO @ Tue, 16 Jun 2020 09:07:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.10_summits.bed INFO @ Tue, 16 Jun 2020 09:07:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1432 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:07:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228848/SRX2228848.20_summits.bed INFO @ Tue, 16 Jun 2020 09:07:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (627 records, 4 fields): 2 millis CompletedMACS2peakCalling