Job ID = 6367841 SRX = SRX4085409 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:52:03 prefetch.2.10.7: 1) Downloading 'SRR7167438'... 2020-06-15T23:52:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:48 prefetch.2.10.7: 'SRR7167438' is valid 2020-06-15T23:53:48 prefetch.2.10.7: 1) 'SRR7167438' was downloaded successfully Read 6110196 spots for SRR7167438/SRR7167438.sra Written 6110196 spots for SRR7167438/SRR7167438.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: 00:02:37 6110196 reads; of these: 6110196 (100.00%) were paired; of these: 4194705 (68.65%) aligned concordantly 0 times 1651392 (27.03%) aligned concordantly exactly 1 time 264099 (4.32%) aligned concordantly >1 times ---- 4194705 pairs aligned concordantly 0 times; of these: 78171 (1.86%) aligned discordantly 1 time ---- 4116534 pairs aligned 0 times concordantly or discordantly; of these: 8233068 mates make up the pairs; of these: 7076636 (85.95%) aligned 0 times 1031539 (12.53%) aligned exactly 1 time 124893 (1.52%) aligned >1 times 42.09% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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_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] 156954 / 1968007 = 0.0798 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 08:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.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 08:59:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:07: 1000000 INFO @ Tue, 16 Jun 2020 08:59:12: 2000000 INFO @ Tue, 16 Jun 2020 08:59:16: 3000000 INFO @ Tue, 16 Jun 2020 08:59:21: 4000000 INFO @ Tue, 16 Jun 2020 08:59:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:59:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:59:25: #1 total tags in treatment: 1765612 INFO @ Tue, 16 Jun 2020 08:59:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:25: #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 08:59:25: #1 tags after filtering in treatment: 1594117 INFO @ Tue, 16 Jun 2020 08:59:25: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:59:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:25: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 08:59:25: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 08:59:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:25: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 08:59:25: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 16 Jun 2020 08:59:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.05_model.r WARNING @ Tue, 16 Jun 2020 08:59:25: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:59:25: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 16 Jun 2020 08:59:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:59:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:29: #3 Call peaks for each chromosome... 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 08:59:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.05_summits.bed INFO @ Tue, 16 Jun 2020 08:59:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:59:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.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 08:59:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:37: 1000000 INFO @ Tue, 16 Jun 2020 08:59:43: 2000000 INFO @ Tue, 16 Jun 2020 08:59:48: 3000000 INFO @ Tue, 16 Jun 2020 08:59:53: 4000000 INFO @ Tue, 16 Jun 2020 08:59:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:59:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:59:58: #1 total tags in treatment: 1765612 INFO @ Tue, 16 Jun 2020 08:59:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:58: #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 08:59:58: #1 tags after filtering in treatment: 1594117 INFO @ Tue, 16 Jun 2020 08:59:58: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:59:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:58: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 08:59:58: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 08:59:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:58: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 08:59:58: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 16 Jun 2020 08:59:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.10_model.r WARNING @ Tue, 16 Jun 2020 08:59:58: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:59:58: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 16 Jun 2020 08:59:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:59:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:58: #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 09:00:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.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 09:00:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.10_summits.bed INFO @ Tue, 16 Jun 2020 09:00:03: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:00:07: 1000000 INFO @ Tue, 16 Jun 2020 09:00:12: 2000000 INFO @ Tue, 16 Jun 2020 09:00:16: 3000000 INFO @ Tue, 16 Jun 2020 09:00:21: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:00:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:00:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:00:25: #1 total tags in treatment: 1765612 INFO @ Tue, 16 Jun 2020 09:00:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:25: #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 09:00:25: #1 tags after filtering in treatment: 1594117 INFO @ Tue, 16 Jun 2020 09:00:25: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:00:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:25: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 09:00:25: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:25: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:00:25: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 16 Jun 2020 09:00:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.20_model.r WARNING @ Tue, 16 Jun 2020 09:00:25: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:25: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 16 Jun 2020 09:00:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:00:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085409/SRX4085409.20_summits.bed INFO @ Tue, 16 Jun 2020 09:00:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (42 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。