Job ID = 6368071 SRX = SRX466534 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:01:00 prefetch.2.10.7: 1) Downloading 'SRR1163600'... 2020-06-16T00:01:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:02:58 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:02:58 prefetch.2.10.7: 1) 'SRR1163600' was downloaded successfully Read 16090826 spots for SRR1163600/SRR1163600.sra Written 16090826 spots for SRR1163600/SRR1163600.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: 00:03:01 16090826 reads; of these: 16090826 (100.00%) were unpaired; of these: 155898 (0.97%) aligned 0 times 13499161 (83.89%) aligned exactly 1 time 2435767 (15.14%) aligned >1 times 99.03% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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_rmdupse_core] 2344077 / 15934928 = 0.1471 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 09:10:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.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 09:10:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:38: 1000000 INFO @ Tue, 16 Jun 2020 09:10:43: 2000000 INFO @ Tue, 16 Jun 2020 09:10:49: 3000000 INFO @ Tue, 16 Jun 2020 09:10:54: 4000000 INFO @ Tue, 16 Jun 2020 09:11:00: 5000000 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 09:11:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.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 09:11:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:06: 6000000 INFO @ Tue, 16 Jun 2020 09:11:08: 1000000 INFO @ Tue, 16 Jun 2020 09:11:12: 7000000 INFO @ Tue, 16 Jun 2020 09:11:15: 2000000 INFO @ Tue, 16 Jun 2020 09:11:19: 8000000 INFO @ Tue, 16 Jun 2020 09:11:21: 3000000 INFO @ Tue, 16 Jun 2020 09:11:25: 9000000 INFO @ Tue, 16 Jun 2020 09:11:28: 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 09:11:32: 10000000 INFO @ Tue, 16 Jun 2020 09:11:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.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 09:11:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:34: 5000000 INFO @ Tue, 16 Jun 2020 09:11:38: 11000000 INFO @ Tue, 16 Jun 2020 09:11:39: 1000000 INFO @ Tue, 16 Jun 2020 09:11:41: 6000000 INFO @ Tue, 16 Jun 2020 09:11:45: 12000000 INFO @ Tue, 16 Jun 2020 09:11:46: 2000000 INFO @ Tue, 16 Jun 2020 09:11:47: 7000000 INFO @ Tue, 16 Jun 2020 09:11:51: 13000000 INFO @ Tue, 16 Jun 2020 09:11:53: 3000000 INFO @ Tue, 16 Jun 2020 09:11:54: 8000000 INFO @ Tue, 16 Jun 2020 09:11:55: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:11:55: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:11:55: #1 total tags in treatment: 13590851 INFO @ Tue, 16 Jun 2020 09:11:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:55: #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 09:11:56: #1 tags after filtering in treatment: 13590851 INFO @ Tue, 16 Jun 2020 09:11:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:57: #2 number of paired peaks: 186 WARNING @ Tue, 16 Jun 2020 09:11:57: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:57: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:11:57: #2 alternative fragment length(s) may be 2,40,554,580 bps INFO @ Tue, 16 Jun 2020 09:11:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:57: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:57: #2 You may need to consider one of the other alternative d(s): 2,40,554,580 WARNING @ Tue, 16 Jun 2020 09:11:57: #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 09:11:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:01: 9000000 INFO @ Tue, 16 Jun 2020 09:12:01: 4000000 INFO @ Tue, 16 Jun 2020 09:12:07: 10000000 INFO @ Tue, 16 Jun 2020 09:12:08: 5000000 INFO @ Tue, 16 Jun 2020 09:12:14: 11000000 INFO @ Tue, 16 Jun 2020 09:12:15: 6000000 INFO @ Tue, 16 Jun 2020 09:12:20: 12000000 INFO @ Tue, 16 Jun 2020 09:12:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:22: 7000000 INFO @ Tue, 16 Jun 2020 09:12:27: 13000000 INFO @ Tue, 16 Jun 2020 09:12:29: 8000000 INFO @ Tue, 16 Jun 2020 09:12:31: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:31: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:31: #1 total tags in treatment: 13590851 INFO @ Tue, 16 Jun 2020 09:12:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:31: #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 09:12:31: #1 tags after filtering in treatment: 13590851 INFO @ Tue, 16 Jun 2020 09:12:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:32: #2 number of paired peaks: 186 WARNING @ Tue, 16 Jun 2020 09:12:32: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:32: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:12:32: #2 alternative fragment length(s) may be 2,40,554,580 bps INFO @ Tue, 16 Jun 2020 09:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:32: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:32: #2 You may need to consider one of the other alternative d(s): 2,40,554,580 WARNING @ Tue, 16 Jun 2020 09:12:32: #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 09:12:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (624 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:35: 9000000 INFO @ Tue, 16 Jun 2020 09:12:41: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:47: 11000000 INFO @ Tue, 16 Jun 2020 09:12:53: 12000000 INFO @ Tue, 16 Jun 2020 09:12:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:58: 13000000 INFO @ Tue, 16 Jun 2020 09:13:02: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:13:02: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:13:02: #1 total tags in treatment: 13590851 INFO @ Tue, 16 Jun 2020 09:13:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:02: #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 09:13:02: #1 tags after filtering in treatment: 13590851 INFO @ Tue, 16 Jun 2020 09:13:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:03: #2 number of paired peaks: 186 WARNING @ Tue, 16 Jun 2020 09:13:03: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:03: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:13:03: #2 alternative fragment length(s) may be 2,40,554,580 bps INFO @ Tue, 16 Jun 2020 09:13:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.20_model.r WARNING @ Tue, 16 Jun 2020 09:13:03: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:03: #2 You may need to consider one of the other alternative d(s): 2,40,554,580 WARNING @ Tue, 16 Jun 2020 09:13:03: #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 09:13:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (282 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466534/SRX466534.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 1 millis CompletedMACS2peakCalling