Job ID = 6366705 SRX = SRX2228860 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:56:14 prefetch.2.10.7: 1) Downloading 'SRR4380316'... 2020-06-15T22:56:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:35 prefetch.2.10.7: 1) 'SRR4380316' was downloaded successfully Read 15555360 spots for SRR4380316/SRR4380316.sra Written 15555360 spots for SRR4380316/SRR4380316.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: 00:03:22 15555360 reads; of these: 15555360 (100.00%) were unpaired; of these: 2141862 (13.77%) aligned 0 times 11142991 (71.63%) aligned exactly 1 time 2270507 (14.60%) aligned >1 times 86.23% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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] 2258783 / 13413498 = 0.1684 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 08:05:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.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 08:05:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:43: 1000000 INFO @ Tue, 16 Jun 2020 08:05:48: 2000000 INFO @ Tue, 16 Jun 2020 08:05:53: 3000000 INFO @ Tue, 16 Jun 2020 08:05:58: 4000000 INFO @ Tue, 16 Jun 2020 08:06:03: 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 08:06:08: 6000000 INFO @ Tue, 16 Jun 2020 08:06:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.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 08:06:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:13: 7000000 INFO @ Tue, 16 Jun 2020 08:06:13: 1000000 INFO @ Tue, 16 Jun 2020 08:06:18: 8000000 INFO @ Tue, 16 Jun 2020 08:06:19: 2000000 INFO @ Tue, 16 Jun 2020 08:06:23: 9000000 INFO @ Tue, 16 Jun 2020 08:06:23: 3000000 INFO @ Tue, 16 Jun 2020 08:06:28: 10000000 INFO @ Tue, 16 Jun 2020 08:06:28: 4000000 INFO @ Tue, 16 Jun 2020 08:06:33: 11000000 INFO @ Tue, 16 Jun 2020 08:06:33: 5000000 INFO @ Tue, 16 Jun 2020 08:06:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:34: #1 total tags in treatment: 11154715 INFO @ Tue, 16 Jun 2020 08:06:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:34: #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 08:06:34: #1 tags after filtering in treatment: 11154715 INFO @ Tue, 16 Jun 2020 08:06:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:35: #2 number of paired peaks: 377 WARNING @ Tue, 16 Jun 2020 08:06:35: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:35: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 08:06:35: #2 alternative fragment length(s) may be 91,113 bps INFO @ Tue, 16 Jun 2020 08:06:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.05_model.r INFO @ Tue, 16 Jun 2020 08:06:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:35: #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 08:06:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.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 08:06:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:38: 6000000 INFO @ Tue, 16 Jun 2020 08:06:43: 7000000 INFO @ Tue, 16 Jun 2020 08:06:43: 1000000 INFO @ Tue, 16 Jun 2020 08:06:48: 8000000 INFO @ Tue, 16 Jun 2020 08:06:49: 2000000 INFO @ Tue, 16 Jun 2020 08:06:53: 9000000 INFO @ Tue, 16 Jun 2020 08:06:54: 3000000 INFO @ Tue, 16 Jun 2020 08:06:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:58: 10000000 INFO @ Tue, 16 Jun 2020 08:06:59: 4000000 INFO @ Tue, 16 Jun 2020 08:07:03: 11000000 INFO @ Tue, 16 Jun 2020 08:07:04: 5000000 INFO @ Tue, 16 Jun 2020 08:07:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:04: #1 total tags in treatment: 11154715 INFO @ Tue, 16 Jun 2020 08:07:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:04: #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 08:07:04: #1 tags after filtering in treatment: 11154715 INFO @ Tue, 16 Jun 2020 08:07:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:05: #2 number of paired peaks: 377 WARNING @ Tue, 16 Jun 2020 08:07:05: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:05: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 08:07:05: #2 alternative fragment length(s) may be 91,113 bps INFO @ Tue, 16 Jun 2020 08:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.10_model.r INFO @ Tue, 16 Jun 2020 08:07:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:09: 6000000 INFO @ Tue, 16 Jun 2020 08:07:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.05_summits.bed INFO @ Tue, 16 Jun 2020 08:07:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1823 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:14: 7000000 INFO @ Tue, 16 Jun 2020 08:07:19: 8000000 INFO @ Tue, 16 Jun 2020 08:07:24: 9000000 INFO @ Tue, 16 Jun 2020 08:07:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:29: 10000000 INFO @ Tue, 16 Jun 2020 08:07:34: 11000000 INFO @ Tue, 16 Jun 2020 08:07:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:34: #1 total tags in treatment: 11154715 INFO @ Tue, 16 Jun 2020 08:07:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:34: #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 08:07:35: #1 tags after filtering in treatment: 11154715 INFO @ Tue, 16 Jun 2020 08:07:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:35: #2 number of paired peaks: 377 WARNING @ Tue, 16 Jun 2020 08:07:35: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:35: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 08:07:35: #2 alternative fragment length(s) may be 91,113 bps INFO @ Tue, 16 Jun 2020 08:07:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.20_model.r INFO @ Tue, 16 Jun 2020 08:07:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (992 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:07:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:08:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228860/SRX2228860.20_summits.bed INFO @ Tue, 16 Jun 2020 08:08:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 1 millis CompletedMACS2peakCalling