Job ID = 6367788 SRX = SRX4085356 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:52:48 prefetch.2.10.7: 1) Downloading 'SRR7167385'... 2020-06-15T23:52:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:55:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:55:56 prefetch.2.10.7: 1) 'SRR7167385' was downloaded successfully Read 12039430 spots for SRR7167385/SRR7167385.sra Written 12039430 spots for SRR7167385/SRR7167385.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: 00:10:02 12039430 reads; of these: 12039430 (100.00%) were paired; of these: 556768 (4.62%) aligned concordantly 0 times 10053946 (83.51%) aligned concordantly exactly 1 time 1428716 (11.87%) aligned concordantly >1 times ---- 556768 pairs aligned concordantly 0 times; of these: 46201 (8.30%) aligned discordantly 1 time ---- 510567 pairs aligned 0 times concordantly or discordantly; of these: 1021134 mates make up the pairs; of these: 566204 (55.45%) aligned 0 times 358593 (35.12%) aligned exactly 1 time 96337 (9.43%) aligned >1 times 97.65% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 3802764 / 11513054 = 0.3303 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 09:13:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.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 09:13:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:43: 1000000 INFO @ Tue, 16 Jun 2020 09:13:50: 2000000 INFO @ Tue, 16 Jun 2020 09:13:59: 3000000 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 09:14:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.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 09:14:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:07: 4000000 INFO @ Tue, 16 Jun 2020 09:14:12: 1000000 INFO @ Tue, 16 Jun 2020 09:14:16: 5000000 INFO @ Tue, 16 Jun 2020 09:14:20: 2000000 INFO @ Tue, 16 Jun 2020 09:14:24: 6000000 INFO @ Tue, 16 Jun 2020 09:14:28: 3000000 INFO @ Tue, 16 Jun 2020 09:14:33: 7000000 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 09:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.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 09:14:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:35: 4000000 INFO @ Tue, 16 Jun 2020 09:14:41: 8000000 INFO @ Tue, 16 Jun 2020 09:14:43: 1000000 INFO @ Tue, 16 Jun 2020 09:14:43: 5000000 INFO @ Tue, 16 Jun 2020 09:14:50: 9000000 INFO @ Tue, 16 Jun 2020 09:14:51: 2000000 INFO @ Tue, 16 Jun 2020 09:14:51: 6000000 INFO @ Tue, 16 Jun 2020 09:14:58: 10000000 INFO @ Tue, 16 Jun 2020 09:14:58: 3000000 INFO @ Tue, 16 Jun 2020 09:14:59: 7000000 INFO @ Tue, 16 Jun 2020 09:15:06: 4000000 INFO @ Tue, 16 Jun 2020 09:15:07: 11000000 INFO @ Tue, 16 Jun 2020 09:15:07: 8000000 INFO @ Tue, 16 Jun 2020 09:15:14: 5000000 INFO @ Tue, 16 Jun 2020 09:15:14: 9000000 INFO @ Tue, 16 Jun 2020 09:15:15: 12000000 INFO @ Tue, 16 Jun 2020 09:15:22: 6000000 INFO @ Tue, 16 Jun 2020 09:15:22: 10000000 INFO @ Tue, 16 Jun 2020 09:15:23: 13000000 INFO @ Tue, 16 Jun 2020 09:15:29: 7000000 INFO @ Tue, 16 Jun 2020 09:15:30: 11000000 INFO @ Tue, 16 Jun 2020 09:15:31: 14000000 INFO @ Tue, 16 Jun 2020 09:15:37: 8000000 INFO @ Tue, 16 Jun 2020 09:15:38: 12000000 INFO @ Tue, 16 Jun 2020 09:15:39: 15000000 INFO @ Tue, 16 Jun 2020 09:15:45: 9000000 INFO @ Tue, 16 Jun 2020 09:15:45: 13000000 INFO @ Tue, 16 Jun 2020 09:15:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:15:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:15:47: #1 total tags in treatment: 7688343 INFO @ Tue, 16 Jun 2020 09:15:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:47: #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 09:15:47: #1 tags after filtering in treatment: 6770855 INFO @ Tue, 16 Jun 2020 09:15:47: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:15:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:47: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 09:15:47: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:48: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 09:15:48: #2 alternative fragment length(s) may be 4,140,163 bps INFO @ Tue, 16 Jun 2020 09:15:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.05_model.r INFO @ Tue, 16 Jun 2020 09:15:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:52: 10000000 INFO @ Tue, 16 Jun 2020 09:15:53: 14000000 INFO @ Tue, 16 Jun 2020 09:15:59: 11000000 INFO @ Tue, 16 Jun 2020 09:16:00: 15000000 INFO @ Tue, 16 Jun 2020 09:16:03: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:16:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:06: #1 total tags in treatment: 7688343 INFO @ Tue, 16 Jun 2020 09:16:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:06: #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 09:16:06: #1 tags after filtering in treatment: 6770855 INFO @ Tue, 16 Jun 2020 09:16:06: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:16:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:06: 12000000 INFO @ Tue, 16 Jun 2020 09:16:07: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 09:16:07: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:07: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 09:16:07: #2 alternative fragment length(s) may be 4,140,163 bps INFO @ Tue, 16 Jun 2020 09:16:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.10_model.r INFO @ Tue, 16 Jun 2020 09:16:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1012 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:13: 13000000 INFO @ Tue, 16 Jun 2020 09:16:19: 14000000 INFO @ Tue, 16 Jun 2020 09:16:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:25: 15000000 INFO @ Tue, 16 Jun 2020 09:16:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.10_summits.bed INFO @ Tue, 16 Jun 2020 09:16:30: Done! pass1 - making usageList (7 chroms): 0 millis INFO @ Tue, 16 Jun 2020 09:16:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:31: #1 total tags in treatment: 7688343 INFO @ Tue, 16 Jun 2020 09:16:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass2 - checking and writing primary data (572 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:31: #1 tags after filtering in treatment: 6770855 INFO @ Tue, 16 Jun 2020 09:16:31: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:16:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:31: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 09:16:31: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:31: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 09:16:31: #2 alternative fragment length(s) may be 4,140,163 bps INFO @ Tue, 16 Jun 2020 09:16:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.20_model.r INFO @ Tue, 16 Jun 2020 09:16:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:16:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085356/SRX4085356.20_summits.bed INFO @ Tue, 16 Jun 2020 09:16:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (262 records, 4 fields): 1 millis CompletedMACS2peakCalling