Job ID = 6366686 SRX = SRX222639 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:07:23 prefetch.2.10.7: 1) Downloading 'SRR660146'... 2020-06-15T23:07:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:08:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:08:04 prefetch.2.10.7: 'SRR660146' is valid 2020-06-15T23:08:04 prefetch.2.10.7: 1) 'SRR660146' was downloaded successfully Read 6976383 spots for SRR660146/SRR660146.sra Written 6976383 spots for SRR660146/SRR660146.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: 00:01:08 6976383 reads; of these: 6976383 (100.00%) were unpaired; of these: 1196283 (17.15%) aligned 0 times 4904042 (70.29%) aligned exactly 1 time 876058 (12.56%) aligned >1 times 82.85% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 434151 / 5780100 = 0.0751 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 08:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.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 08:11:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:36: 1000000 INFO @ Tue, 16 Jun 2020 08:11:40: 2000000 INFO @ Tue, 16 Jun 2020 08:11:45: 3000000 INFO @ Tue, 16 Jun 2020 08:11:49: 4000000 INFO @ Tue, 16 Jun 2020 08:11:53: 5000000 INFO @ Tue, 16 Jun 2020 08:11:55: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:11:55: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:11:55: #1 total tags in treatment: 5345949 INFO @ Tue, 16 Jun 2020 08:11:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:55: #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 08:11:55: #1 tags after filtering in treatment: 5345949 INFO @ Tue, 16 Jun 2020 08:11:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:55: #2 number of paired peaks: 668 WARNING @ Tue, 16 Jun 2020 08:11:55: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:55: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:11:55: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 08:11:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.05_model.r INFO @ Tue, 16 Jun 2020 08:11:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:55: #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 08:12:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.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 08:12:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:07: 1000000 INFO @ Tue, 16 Jun 2020 08:12:11: 2000000 INFO @ Tue, 16 Jun 2020 08:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.05_summits.bed INFO @ Tue, 16 Jun 2020 08:12:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3833 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:16: 3000000 INFO @ Tue, 16 Jun 2020 08:12:20: 4000000 INFO @ Tue, 16 Jun 2020 08:12:25: 5000000 INFO @ Tue, 16 Jun 2020 08:12:26: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:12:26: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:12:26: #1 total tags in treatment: 5345949 INFO @ Tue, 16 Jun 2020 08:12:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:26: #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 08:12:26: #1 tags after filtering in treatment: 5345949 INFO @ Tue, 16 Jun 2020 08:12:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:27: #2 number of paired peaks: 668 WARNING @ Tue, 16 Jun 2020 08:12:27: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:27: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:12:27: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 08:12:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.10_model.r INFO @ Tue, 16 Jun 2020 08:12:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:27: #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 08:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.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 08:12:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:36: 1000000 INFO @ Tue, 16 Jun 2020 08:12:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:41: 2000000 INFO @ Tue, 16 Jun 2020 08:12:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.10_summits.bed INFO @ Tue, 16 Jun 2020 08:12:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2136 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:45: 3000000 INFO @ Tue, 16 Jun 2020 08:12:50: 4000000 INFO @ Tue, 16 Jun 2020 08:12:54: 5000000 INFO @ Tue, 16 Jun 2020 08:12:55: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:12:55: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:12:55: #1 total tags in treatment: 5345949 INFO @ Tue, 16 Jun 2020 08:12:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:55: #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 08:12:56: #1 tags after filtering in treatment: 5345949 INFO @ Tue, 16 Jun 2020 08:12:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:56: #2 number of paired peaks: 668 WARNING @ Tue, 16 Jun 2020 08:12:56: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:56: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:12:56: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 08:12:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.20_model.r INFO @ Tue, 16 Jun 2020 08:12:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:56: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:13:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.20_peaks.xls BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:13:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX222639/SRX222639.20_summits.bed INFO @ Tue, 16 Jun 2020 08:13:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (904 records, 4 fields): 3 millis CompletedMACS2peakCalling