Job ID = 6366708 SRX = SRX2228863 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:56:29 prefetch.2.10.7: 1) Downloading 'SRR4380319'... 2020-06-15T22:56:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:04 prefetch.2.10.7: 1) 'SRR4380319' was downloaded successfully Read 11982884 spots for SRR4380319/SRR4380319.sra Written 11982884 spots for SRR4380319/SRR4380319.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: 00:03:43 11982884 reads; of these: 11982884 (100.00%) were unpaired; of these: 1115093 (9.31%) aligned 0 times 9281116 (77.45%) aligned exactly 1 time 1586675 (13.24%) aligned >1 times 90.69% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 1918059 / 10867791 = 0.1765 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 08:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.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 08:06:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:34: 1000000 INFO @ Tue, 16 Jun 2020 08:06:40: 2000000 INFO @ Tue, 16 Jun 2020 08:06:46: 3000000 INFO @ Tue, 16 Jun 2020 08:06:52: 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 08:06:58: 5000000 INFO @ Tue, 16 Jun 2020 08:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.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 08:06:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:04: 6000000 INFO @ Tue, 16 Jun 2020 08:07:05: 1000000 INFO @ Tue, 16 Jun 2020 08:07:10: 7000000 INFO @ Tue, 16 Jun 2020 08:07:11: 2000000 INFO @ Tue, 16 Jun 2020 08:07:16: 8000000 INFO @ Tue, 16 Jun 2020 08:07:17: 3000000 INFO @ Tue, 16 Jun 2020 08:07:21: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:07:21: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:07:21: #1 total tags in treatment: 8949732 INFO @ Tue, 16 Jun 2020 08:07:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:21: #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 08:07:21: #1 tags after filtering in treatment: 8949732 INFO @ Tue, 16 Jun 2020 08:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:22: #2 number of paired peaks: 801 WARNING @ Tue, 16 Jun 2020 08:07:22: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:22: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 08:07:22: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 16 Jun 2020 08:07:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.05_model.r INFO @ Tue, 16 Jun 2020 08:07:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:23: 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 08:07:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.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 08:07:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:29: 5000000 INFO @ Tue, 16 Jun 2020 08:07:35: 1000000 INFO @ Tue, 16 Jun 2020 08:07:35: 6000000 INFO @ Tue, 16 Jun 2020 08:07:41: 2000000 INFO @ Tue, 16 Jun 2020 08:07:41: 7000000 INFO @ Tue, 16 Jun 2020 08:07:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:47: 8000000 INFO @ Tue, 16 Jun 2020 08:07:47: 3000000 INFO @ Tue, 16 Jun 2020 08:07:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.05_summits.bed INFO @ Tue, 16 Jun 2020 08:07:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1814 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:52: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:07:52: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:07:52: #1 total tags in treatment: 8949732 INFO @ Tue, 16 Jun 2020 08:07:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:52: #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 08:07:52: #1 tags after filtering in treatment: 8949732 INFO @ Tue, 16 Jun 2020 08:07:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:53: 4000000 INFO @ Tue, 16 Jun 2020 08:07:53: #2 number of paired peaks: 801 WARNING @ Tue, 16 Jun 2020 08:07:53: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:53: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 08:07:53: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 16 Jun 2020 08:07:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.10_model.r INFO @ Tue, 16 Jun 2020 08:07:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:58: 5000000 INFO @ Tue, 16 Jun 2020 08:08:04: 6000000 INFO @ Tue, 16 Jun 2020 08:08:10: 7000000 INFO @ Tue, 16 Jun 2020 08:08:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:15: 8000000 INFO @ Tue, 16 Jun 2020 08:08:21: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:08:21: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:08:21: #1 total tags in treatment: 8949732 INFO @ Tue, 16 Jun 2020 08:08:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:21: #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 08:08:21: #1 tags after filtering in treatment: 8949732 INFO @ Tue, 16 Jun 2020 08:08:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:21: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:21: #2 number of paired peaks: 801 WARNING @ Tue, 16 Jun 2020 08:08:21: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:21: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 08:08:21: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 16 Jun 2020 08:08:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.20_model.r INFO @ Tue, 16 Jun 2020 08:08:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1210 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:08:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228863/SRX2228863.20_summits.bed INFO @ Tue, 16 Jun 2020 08:08:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (769 records, 4 fields): 2 millis CompletedMACS2peakCalling