Job ID = 6366924 SRX = SRX2576627 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:03:38 prefetch.2.10.7: 1) Downloading 'SRR5272584'... 2020-06-15T23:03:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:04:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:04:54 prefetch.2.10.7: 'SRR5272584' is valid 2020-06-15T23:04:54 prefetch.2.10.7: 1) 'SRR5272584' was downloaded successfully Read 20246590 spots for SRR5272584/SRR5272584.sra Written 20246590 spots for SRR5272584/SRR5272584.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: 00:03:20 20246590 reads; of these: 20246590 (100.00%) were unpaired; of these: 340604 (1.68%) aligned 0 times 16368596 (80.85%) aligned exactly 1 time 3537390 (17.47%) aligned >1 times 98.32% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 3821557 / 19905986 = 0.1920 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 08:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.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 08:13:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:54: 1000000 INFO @ Tue, 16 Jun 2020 08:14:00: 2000000 INFO @ Tue, 16 Jun 2020 08:14:06: 3000000 INFO @ Tue, 16 Jun 2020 08:14:11: 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 08:14:17: 5000000 INFO @ Tue, 16 Jun 2020 08:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.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 08:14:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:23: 6000000 INFO @ Tue, 16 Jun 2020 08:14:24: 1000000 INFO @ Tue, 16 Jun 2020 08:14:29: 7000000 INFO @ Tue, 16 Jun 2020 08:14:29: 2000000 INFO @ Tue, 16 Jun 2020 08:14:35: 3000000 INFO @ Tue, 16 Jun 2020 08:14:35: 8000000 INFO @ Tue, 16 Jun 2020 08:14:40: 4000000 INFO @ Tue, 16 Jun 2020 08:14:41: 9000000 INFO @ Tue, 16 Jun 2020 08:14:46: 5000000 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 08:14:47: 10000000 INFO @ Tue, 16 Jun 2020 08:14:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.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 08:14:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:51: 6000000 INFO @ Tue, 16 Jun 2020 08:14:53: 11000000 INFO @ Tue, 16 Jun 2020 08:14:54: 1000000 INFO @ Tue, 16 Jun 2020 08:14:57: 7000000 INFO @ Tue, 16 Jun 2020 08:14:59: 2000000 INFO @ Tue, 16 Jun 2020 08:14:59: 12000000 INFO @ Tue, 16 Jun 2020 08:15:03: 8000000 INFO @ Tue, 16 Jun 2020 08:15:05: 3000000 INFO @ Tue, 16 Jun 2020 08:15:05: 13000000 INFO @ Tue, 16 Jun 2020 08:15:08: 9000000 INFO @ Tue, 16 Jun 2020 08:15:10: 4000000 INFO @ Tue, 16 Jun 2020 08:15:11: 14000000 INFO @ Tue, 16 Jun 2020 08:15:14: 10000000 INFO @ Tue, 16 Jun 2020 08:15:16: 5000000 INFO @ Tue, 16 Jun 2020 08:15:17: 15000000 INFO @ Tue, 16 Jun 2020 08:15:19: 11000000 INFO @ Tue, 16 Jun 2020 08:15:21: 6000000 INFO @ Tue, 16 Jun 2020 08:15:23: 16000000 INFO @ Tue, 16 Jun 2020 08:15:24: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:15:24: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:15:24: #1 total tags in treatment: 16084429 INFO @ Tue, 16 Jun 2020 08:15:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:24: #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 08:15:24: #1 tags after filtering in treatment: 16084429 INFO @ Tue, 16 Jun 2020 08:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:25: 12000000 INFO @ Tue, 16 Jun 2020 08:15:25: #2 number of paired peaks: 470 WARNING @ Tue, 16 Jun 2020 08:15:25: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:25: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:15:25: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:15:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.05_model.r INFO @ Tue, 16 Jun 2020 08:15:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:27: 7000000 INFO @ Tue, 16 Jun 2020 08:15:31: 13000000 INFO @ Tue, 16 Jun 2020 08:15:32: 8000000 INFO @ Tue, 16 Jun 2020 08:15:36: 14000000 INFO @ Tue, 16 Jun 2020 08:15:38: 9000000 INFO @ Tue, 16 Jun 2020 08:15:42: 15000000 INFO @ Tue, 16 Jun 2020 08:15:43: 10000000 INFO @ Tue, 16 Jun 2020 08:15:47: 16000000 INFO @ Tue, 16 Jun 2020 08:15:48: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:15:48: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:15:48: #1 total tags in treatment: 16084429 INFO @ Tue, 16 Jun 2020 08:15:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:48: #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 08:15:48: #1 tags after filtering in treatment: 16084429 INFO @ Tue, 16 Jun 2020 08:15:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:49: 11000000 INFO @ Tue, 16 Jun 2020 08:15:49: #2 number of paired peaks: 470 WARNING @ Tue, 16 Jun 2020 08:15:49: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:50: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:15:50: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.10_model.r INFO @ Tue, 16 Jun 2020 08:15:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:54: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:15:59: 13000000 INFO @ Tue, 16 Jun 2020 08:16:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:05: 14000000 INFO @ Tue, 16 Jun 2020 08:16:10: 15000000 INFO @ Tue, 16 Jun 2020 08:16:15: 16000000 INFO @ Tue, 16 Jun 2020 08:16:15: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:16:15: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:16:15: #1 total tags in treatment: 16084429 INFO @ Tue, 16 Jun 2020 08:16:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:15: #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 08:16:16: #1 tags after filtering in treatment: 16084429 INFO @ Tue, 16 Jun 2020 08:16:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.05_summits.bed INFO @ Tue, 16 Jun 2020 08:16:16: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2711 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:17: #2 number of paired peaks: 470 WARNING @ Tue, 16 Jun 2020 08:16:17: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:17: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:16:17: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.20_model.r INFO @ Tue, 16 Jun 2020 08:16:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.10_summits.bed INFO @ Tue, 16 Jun 2020 08:16:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1967 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576627/SRX2576627.20_summits.bed INFO @ Tue, 16 Jun 2020 08:17:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1391 records, 4 fields): 2 millis CompletedMACS2peakCalling