Job ID = 6507795 SRX = SRX4085422 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:10:06 prefetch.2.10.7: 1) Downloading 'SRR7167451'... 2020-06-26T13:10:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:13:58 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:13:58 prefetch.2.10.7: 1) 'SRR7167451' was downloaded successfully Read 15275286 spots for SRR7167451/SRR7167451.sra Written 15275286 spots for SRR7167451/SRR7167451.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: 00:08:44 15275286 reads; of these: 15275286 (100.00%) were paired; of these: 8905147 (58.30%) aligned concordantly 0 times 5409722 (35.41%) aligned concordantly exactly 1 time 960417 (6.29%) aligned concordantly >1 times ---- 8905147 pairs aligned concordantly 0 times; of these: 324560 (3.64%) aligned discordantly 1 time ---- 8580587 pairs aligned 0 times concordantly or discordantly; of these: 17161174 mates make up the pairs; of these: 13033020 (75.94%) aligned 0 times 3681952 (21.46%) aligned exactly 1 time 446202 (2.60%) aligned >1 times 57.34% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 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_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] 453853 / 6581646 = 0.0690 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 @ Fri, 26 Jun 2020 22:29:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.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 @ Fri, 26 Jun 2020 22:29:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:54: 1000000 INFO @ Fri, 26 Jun 2020 22:30:00: 2000000 INFO @ Fri, 26 Jun 2020 22:30:06: 3000000 INFO @ Fri, 26 Jun 2020 22:30:11: 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 @ Fri, 26 Jun 2020 22:30:17: 5000000 INFO @ Fri, 26 Jun 2020 22:30:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.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 @ Fri, 26 Jun 2020 22:30:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:30:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:30:24: 6000000 INFO @ Fri, 26 Jun 2020 22:30:25: 1000000 INFO @ Fri, 26 Jun 2020 22:30:30: 7000000 INFO @ Fri, 26 Jun 2020 22:30:31: 2000000 INFO @ Fri, 26 Jun 2020 22:30:36: 8000000 INFO @ Fri, 26 Jun 2020 22:30:38: 3000000 INFO @ Fri, 26 Jun 2020 22:30:42: 9000000 INFO @ Fri, 26 Jun 2020 22:30:44: 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 @ Fri, 26 Jun 2020 22:30:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.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 @ Fri, 26 Jun 2020 22:30:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:30:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:30:49: 10000000 INFO @ Fri, 26 Jun 2020 22:30:51: 5000000 INFO @ Fri, 26 Jun 2020 22:30:55: 1000000 INFO @ Fri, 26 Jun 2020 22:30:56: 11000000 INFO @ Fri, 26 Jun 2020 22:30:58: 6000000 INFO @ Fri, 26 Jun 2020 22:31:02: 2000000 INFO @ Fri, 26 Jun 2020 22:31:02: 12000000 INFO @ Fri, 26 Jun 2020 22:31:05: 7000000 INFO @ Fri, 26 Jun 2020 22:31:09: 3000000 INFO @ Fri, 26 Jun 2020 22:31:09: 13000000 INFO @ Fri, 26 Jun 2020 22:31:11: 8000000 INFO @ Fri, 26 Jun 2020 22:31:16: 4000000 INFO @ Fri, 26 Jun 2020 22:31:16: 14000000 INFO @ Fri, 26 Jun 2020 22:31:18: 9000000 INFO @ Fri, 26 Jun 2020 22:31:23: 5000000 INFO @ Fri, 26 Jun 2020 22:31:23: 15000000 INFO @ Fri, 26 Jun 2020 22:31:24: 10000000 INFO @ Fri, 26 Jun 2020 22:31:30: 16000000 INFO @ Fri, 26 Jun 2020 22:31:30: 6000000 INFO @ Fri, 26 Jun 2020 22:31:31: 11000000 INFO @ Fri, 26 Jun 2020 22:31:34: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:31:34: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:31:34: #1 total tags in treatment: 5928219 INFO @ Fri, 26 Jun 2020 22:31:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:31:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:31:34: #1 tags after filtering in treatment: 5192715 INFO @ Fri, 26 Jun 2020 22:31:34: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 22:31:34: #1 finished! INFO @ Fri, 26 Jun 2020 22:31:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:31:34: #2 number of paired peaks: 546 WARNING @ Fri, 26 Jun 2020 22:31:34: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Fri, 26 Jun 2020 22:31:34: start model_add_line... INFO @ Fri, 26 Jun 2020 22:31:34: start X-correlation... INFO @ Fri, 26 Jun 2020 22:31:34: end of X-cor INFO @ Fri, 26 Jun 2020 22:31:34: #2 finished! INFO @ Fri, 26 Jun 2020 22:31:34: #2 predicted fragment length is 86 bps INFO @ Fri, 26 Jun 2020 22:31:34: #2 alternative fragment length(s) may be 86 bps INFO @ Fri, 26 Jun 2020 22:31:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.05_model.r WARNING @ Fri, 26 Jun 2020 22:31:35: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:31:35: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Fri, 26 Jun 2020 22:31:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:31:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:31:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:31:37: 7000000 INFO @ Fri, 26 Jun 2020 22:31:38: 12000000 INFO @ Fri, 26 Jun 2020 22:31:43: 8000000 INFO @ Fri, 26 Jun 2020 22:31:44: 13000000 INFO @ Fri, 26 Jun 2020 22:31:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:31:50: 9000000 INFO @ Fri, 26 Jun 2020 22:31:51: 14000000 INFO @ Fri, 26 Jun 2020 22:31:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:31:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:31:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.05_summits.bed INFO @ Fri, 26 Jun 2020 22:31:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3562 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:31:56: 10000000 INFO @ Fri, 26 Jun 2020 22:31:57: 15000000 INFO @ Fri, 26 Jun 2020 22:32:02: 11000000 INFO @ Fri, 26 Jun 2020 22:32:04: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:32:07: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:32:07: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:32:07: #1 total tags in treatment: 5928219 INFO @ Fri, 26 Jun 2020 22:32:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:32:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:32:08: #1 tags after filtering in treatment: 5192715 INFO @ Fri, 26 Jun 2020 22:32:08: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 22:32:08: #1 finished! INFO @ Fri, 26 Jun 2020 22:32:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:32:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:32:08: #2 number of paired peaks: 546 WARNING @ Fri, 26 Jun 2020 22:32:08: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Fri, 26 Jun 2020 22:32:08: start model_add_line... INFO @ Fri, 26 Jun 2020 22:32:08: start X-correlation... INFO @ Fri, 26 Jun 2020 22:32:08: end of X-cor INFO @ Fri, 26 Jun 2020 22:32:08: #2 finished! INFO @ Fri, 26 Jun 2020 22:32:08: #2 predicted fragment length is 86 bps INFO @ Fri, 26 Jun 2020 22:32:08: #2 alternative fragment length(s) may be 86 bps INFO @ Fri, 26 Jun 2020 22:32:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.10_model.r WARNING @ Fri, 26 Jun 2020 22:32:08: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:32:08: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Fri, 26 Jun 2020 22:32:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:32:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:32:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:32:08: 12000000 INFO @ Fri, 26 Jun 2020 22:32:14: 13000000 INFO @ Fri, 26 Jun 2020 22:32:20: 14000000 INFO @ Fri, 26 Jun 2020 22:32:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:32:25: 15000000 INFO @ Fri, 26 Jun 2020 22:32:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:32:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:32:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.10_summits.bed INFO @ Fri, 26 Jun 2020 22:32:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1816 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:32:31: 16000000 INFO @ Fri, 26 Jun 2020 22:32:34: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:32:34: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:32:34: #1 total tags in treatment: 5928219 INFO @ Fri, 26 Jun 2020 22:32:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:32:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:32:34: #1 tags after filtering in treatment: 5192715 INFO @ Fri, 26 Jun 2020 22:32:34: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 22:32:34: #1 finished! INFO @ Fri, 26 Jun 2020 22:32:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:32:34: #2 number of paired peaks: 546 WARNING @ Fri, 26 Jun 2020 22:32:34: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Fri, 26 Jun 2020 22:32:34: start model_add_line... INFO @ Fri, 26 Jun 2020 22:32:34: start X-correlation... INFO @ Fri, 26 Jun 2020 22:32:34: end of X-cor INFO @ Fri, 26 Jun 2020 22:32:34: #2 finished! INFO @ Fri, 26 Jun 2020 22:32:34: #2 predicted fragment length is 86 bps INFO @ Fri, 26 Jun 2020 22:32:34: #2 alternative fragment length(s) may be 86 bps INFO @ Fri, 26 Jun 2020 22:32:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.20_model.r WARNING @ Fri, 26 Jun 2020 22:32:34: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:32:34: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Fri, 26 Jun 2020 22:32:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:32:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:32:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:32:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:32:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:32:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:32:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085422/SRX4085422.20_summits.bed INFO @ Fri, 26 Jun 2020 22:32:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (614 records, 4 fields): 3 millis CompletedMACS2peakCalling