Job ID = 6366310 SRX = SRX1099837 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:46:07 prefetch.2.10.7: 1) Downloading 'SRR2105906'... 2020-06-15T22:46:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:14 prefetch.2.10.7: 'SRR2105906' is valid 2020-06-15T22:47:14 prefetch.2.10.7: 1) 'SRR2105906' was downloaded successfully Read 9026289 spots for SRR2105906/SRR2105906.sra Written 9026289 spots for SRR2105906/SRR2105906.sra 2020-06-15T22:47:52 prefetch.2.10.7: 1) Downloading 'SRR2105907'... 2020-06-15T22:47:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:25 prefetch.2.10.7: 'SRR2105907' is valid 2020-06-15T22:49:25 prefetch.2.10.7: 1) 'SRR2105907' was downloaded successfully Read 11017670 spots for SRR2105907/SRR2105907.sra Written 11017670 spots for SRR2105907/SRR2105907.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: 00:03:57 20043959 reads; of these: 20043959 (100.00%) were unpaired; of these: 3941644 (19.66%) aligned 0 times 13825901 (68.98%) aligned exactly 1 time 2276414 (11.36%) aligned >1 times 80.34% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 5838418 / 16102315 = 0.3626 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 07:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.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 07:58:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:11: 1000000 INFO @ Tue, 16 Jun 2020 07:58:17: 2000000 INFO @ Tue, 16 Jun 2020 07:58:23: 3000000 INFO @ Tue, 16 Jun 2020 07:58:29: 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 07:58:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.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 07:58:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:36: 5000000 INFO @ Tue, 16 Jun 2020 07:58:42: 1000000 INFO @ Tue, 16 Jun 2020 07:58:43: 6000000 INFO @ Tue, 16 Jun 2020 07:58:50: 2000000 INFO @ Tue, 16 Jun 2020 07:58:51: 7000000 INFO @ Tue, 16 Jun 2020 07:58:58: 3000000 INFO @ Tue, 16 Jun 2020 07:58:58: 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 07:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.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 07:59:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:06: 4000000 INFO @ Tue, 16 Jun 2020 07:59:06: 9000000 INFO @ Tue, 16 Jun 2020 07:59:12: 1000000 INFO @ Tue, 16 Jun 2020 07:59:14: 5000000 INFO @ Tue, 16 Jun 2020 07:59:14: 10000000 INFO @ Tue, 16 Jun 2020 07:59:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:59:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:59:16: #1 total tags in treatment: 10263897 INFO @ Tue, 16 Jun 2020 07:59:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:16: #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 07:59:16: #1 tags after filtering in treatment: 10263897 INFO @ Tue, 16 Jun 2020 07:59:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:16: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:17: #2 number of paired peaks: 923 WARNING @ Tue, 16 Jun 2020 07:59:17: Fewer paired peaks (923) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 923 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:17: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:17: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:17: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:17: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:17: #2 predicted fragment length is 199 bps INFO @ Tue, 16 Jun 2020 07:59:17: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 16 Jun 2020 07:59:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.05_model.r INFO @ Tue, 16 Jun 2020 07:59:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:59:20: 2000000 INFO @ Tue, 16 Jun 2020 07:59:21: 6000000 INFO @ Tue, 16 Jun 2020 07:59:28: 3000000 INFO @ Tue, 16 Jun 2020 07:59:29: 7000000 INFO @ Tue, 16 Jun 2020 07:59:35: 4000000 INFO @ Tue, 16 Jun 2020 07:59:37: 8000000 INFO @ Tue, 16 Jun 2020 07:59:43: 5000000 INFO @ Tue, 16 Jun 2020 07:59:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:45: 9000000 INFO @ Tue, 16 Jun 2020 07:59:51: 6000000 INFO @ Tue, 16 Jun 2020 07:59:53: 10000000 INFO @ Tue, 16 Jun 2020 07:59:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:59:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:59:55: #1 total tags in treatment: 10263897 INFO @ Tue, 16 Jun 2020 07:59:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:55: #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 07:59:55: #1 tags after filtering in treatment: 10263897 INFO @ Tue, 16 Jun 2020 07:59:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:55: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:56: #2 number of paired peaks: 923 WARNING @ Tue, 16 Jun 2020 07:59:56: Fewer paired peaks (923) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 923 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:56: #2 predicted fragment length is 199 bps INFO @ Tue, 16 Jun 2020 07:59:56: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 16 Jun 2020 07:59:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.10_model.r INFO @ Tue, 16 Jun 2020 07:59:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:59:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.05_summits.bed INFO @ Tue, 16 Jun 2020 07:59:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4087 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:59:58: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:00:05: 8000000 INFO @ Tue, 16 Jun 2020 08:00:11: 9000000 INFO @ Tue, 16 Jun 2020 08:00:18: 10000000 INFO @ Tue, 16 Jun 2020 08:00:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:00:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:00:19: #1 total tags in treatment: 10263897 INFO @ Tue, 16 Jun 2020 08:00:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:19: #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 08:00:20: #1 tags after filtering in treatment: 10263897 INFO @ Tue, 16 Jun 2020 08:00:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:20: #2 number of paired peaks: 923 WARNING @ Tue, 16 Jun 2020 08:00:20: Fewer paired peaks (923) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 923 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:20: #2 predicted fragment length is 199 bps INFO @ Tue, 16 Jun 2020 08:00:20: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 16 Jun 2020 08:00:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.20_model.r INFO @ Tue, 16 Jun 2020 08:00:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:00:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.10_summits.bed INFO @ Tue, 16 Jun 2020 08:00:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2438 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:00:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099837/SRX1099837.20_summits.bed INFO @ Tue, 16 Jun 2020 08:01:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1317 records, 4 fields): 3 millis CompletedMACS2peakCalling