Job ID = 6366906 SRX = SRX257651 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:07:08 prefetch.2.10.7: 1) Downloading 'SRR800662'... 2020-06-15T23:07:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:08:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:08:35 prefetch.2.10.7: 'SRR800662' is valid 2020-06-15T23:08:35 prefetch.2.10.7: 1) 'SRR800662' was downloaded successfully Read 12994743 spots for SRR800662/SRR800662.sra Written 12994743 spots for SRR800662/SRR800662.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: 00:02:24 12994743 reads; of these: 12994743 (100.00%) were unpaired; of these: 702727 (5.41%) aligned 0 times 10231482 (78.74%) aligned exactly 1 time 2060534 (15.86%) aligned >1 times 94.59% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 4005620 / 12292016 = 0.3259 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 08:14:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.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 08:14:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:45: 1000000 INFO @ Tue, 16 Jun 2020 08:14:50: 2000000 INFO @ Tue, 16 Jun 2020 08:14:55: 3000000 INFO @ Tue, 16 Jun 2020 08:15:00: 4000000 INFO @ Tue, 16 Jun 2020 08:15:05: 5000000 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 08:15:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.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 08:15:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:10: 6000000 INFO @ Tue, 16 Jun 2020 08:15:15: 7000000 INFO @ Tue, 16 Jun 2020 08:15:16: 1000000 INFO @ Tue, 16 Jun 2020 08:15:20: 8000000 INFO @ Tue, 16 Jun 2020 08:15:21: 2000000 INFO @ Tue, 16 Jun 2020 08:15:22: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:15:22: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:15:22: #1 total tags in treatment: 8286396 INFO @ Tue, 16 Jun 2020 08:15:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:22: #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 08:15:22: #1 tags after filtering in treatment: 8286396 INFO @ Tue, 16 Jun 2020 08:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:23: #2 number of paired peaks: 541 WARNING @ Tue, 16 Jun 2020 08:15:23: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:23: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:15:23: #2 alternative fragment length(s) may be 4,123 bps INFO @ Tue, 16 Jun 2020 08:15:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.05_model.r INFO @ Tue, 16 Jun 2020 08:15:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:27: 3000000 INFO @ Tue, 16 Jun 2020 08:15:32: 4000000 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 08:15:38: 5000000 INFO @ Tue, 16 Jun 2020 08:15:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.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 08:15:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:44: 6000000 INFO @ Tue, 16 Jun 2020 08:15:45: 1000000 INFO @ Tue, 16 Jun 2020 08:15:49: 7000000 INFO @ Tue, 16 Jun 2020 08:15:50: 2000000 INFO @ Tue, 16 Jun 2020 08:15:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1810 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:55: 3000000 INFO @ Tue, 16 Jun 2020 08:15:55: 8000000 INFO @ Tue, 16 Jun 2020 08:15:57: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:15:57: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:15:57: #1 total tags in treatment: 8286396 INFO @ Tue, 16 Jun 2020 08:15:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:57: #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 08:15:57: #1 tags after filtering in treatment: 8286396 INFO @ Tue, 16 Jun 2020 08:15:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:58: #2 number of paired peaks: 541 WARNING @ Tue, 16 Jun 2020 08:15:58: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:58: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:15:58: #2 alternative fragment length(s) may be 4,123 bps INFO @ Tue, 16 Jun 2020 08:15:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.10_model.r INFO @ Tue, 16 Jun 2020 08:15:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:00: 4000000 INFO @ Tue, 16 Jun 2020 08:16:05: 5000000 INFO @ Tue, 16 Jun 2020 08:16:10: 6000000 INFO @ Tue, 16 Jun 2020 08:16:15: 7000000 INFO @ Tue, 16 Jun 2020 08:16:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:20: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:21: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:16:21: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:16:21: #1 total tags in treatment: 8286396 INFO @ Tue, 16 Jun 2020 08:16:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:21: #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 08:16:21: #1 tags after filtering in treatment: 8286396 INFO @ Tue, 16 Jun 2020 08:16:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:22: #2 number of paired peaks: 541 WARNING @ Tue, 16 Jun 2020 08:16:22: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:22: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:16:22: #2 alternative fragment length(s) may be 4,123 bps INFO @ Tue, 16 Jun 2020 08:16:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.20_model.r INFO @ Tue, 16 Jun 2020 08:16:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.10_summits.bed INFO @ Tue, 16 Jun 2020 08:16:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (953 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257651/SRX257651.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (442 records, 4 fields): 2 millis CompletedMACS2peakCalling