Job ID = 6366758 SRX = SRX2228911 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:18:46 prefetch.2.10.7: 1) Downloading 'SRR4380367'... 2020-06-15T23:18:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:19:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:19:22 prefetch.2.10.7: 'SRR4380367' is valid 2020-06-15T23:19:22 prefetch.2.10.7: 1) 'SRR4380367' was downloaded successfully Read 6041346 spots for SRR4380367/SRR4380367.sra Written 6041346 spots for SRR4380367/SRR4380367.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: 00:01:55 6041346 reads; of these: 6041346 (100.00%) were unpaired; of these: 1263000 (20.91%) aligned 0 times 3947321 (65.34%) aligned exactly 1 time 831025 (13.76%) aligned >1 times 79.09% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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_rmdupse_core] 1192148 / 4778346 = 0.2495 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 08:23:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.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 08:23:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:37: 1000000 INFO @ Tue, 16 Jun 2020 08:23:44: 2000000 INFO @ Tue, 16 Jun 2020 08:23:51: 3000000 INFO @ Tue, 16 Jun 2020 08:23:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:23:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:23:55: #1 total tags in treatment: 3586198 INFO @ Tue, 16 Jun 2020 08:23:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:55: #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 08:23:56: #1 tags after filtering in treatment: 3586198 INFO @ Tue, 16 Jun 2020 08:23:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:56: #2 number of paired peaks: 513 WARNING @ Tue, 16 Jun 2020 08:23:56: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:56: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 08:23:56: #2 alternative fragment length(s) may be 4,139,179 bps INFO @ Tue, 16 Jun 2020 08:23:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.05_model.r INFO @ Tue, 16 Jun 2020 08:23:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:56: #3 Pre-compute pvalue-qvalue table... 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 08:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.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 08:24:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:07: 1000000 INFO @ Tue, 16 Jun 2020 08:24:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2117 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:14: 2000000 INFO @ Tue, 16 Jun 2020 08:24:20: 3000000 INFO @ Tue, 16 Jun 2020 08:24:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:24:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:24:24: #1 total tags in treatment: 3586198 INFO @ Tue, 16 Jun 2020 08:24:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:24: #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 08:24:24: #1 tags after filtering in treatment: 3586198 INFO @ Tue, 16 Jun 2020 08:24:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:24: #2 number of paired peaks: 513 WARNING @ Tue, 16 Jun 2020 08:24:24: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:24: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 08:24:24: #2 alternative fragment length(s) may be 4,139,179 bps INFO @ Tue, 16 Jun 2020 08:24:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.10_model.r INFO @ Tue, 16 Jun 2020 08:24:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:24: #3 Pre-compute pvalue-qvalue table... 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 08:24:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.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 08:24:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:37: 1000000 INFO @ Tue, 16 Jun 2020 08:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.10_summits.bed INFO @ Tue, 16 Jun 2020 08:24:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (517 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:44: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:24:51: 3000000 INFO @ Tue, 16 Jun 2020 08:24:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:24:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:24:55: #1 total tags in treatment: 3586198 INFO @ Tue, 16 Jun 2020 08:24:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:55: #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 08:24:55: #1 tags after filtering in treatment: 3586198 INFO @ Tue, 16 Jun 2020 08:24:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:56: #2 number of paired peaks: 513 WARNING @ Tue, 16 Jun 2020 08:24:56: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:56: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 08:24:56: #2 alternative fragment length(s) may be 4,139,179 bps INFO @ Tue, 16 Jun 2020 08:24:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.20_model.r INFO @ Tue, 16 Jun 2020 08:24:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:25:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228911/SRX2228911.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (102 records, 4 fields): 2 millis CompletedMACS2peakCalling