Job ID = 6368215 SRX = SRX494898 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:05:46 prefetch.2.10.7: 1) Downloading 'SRR1198430'... 2020-06-16T00:05:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:10:59 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:10:59 prefetch.2.10.7: 1) 'SRR1198430' was downloaded successfully Read 16047878 spots for SRR1198430/SRR1198430.sra Written 16047878 spots for SRR1198430/SRR1198430.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: 00:03:02 16047878 reads; of these: 16047878 (100.00%) were unpaired; of these: 1451130 (9.04%) aligned 0 times 12366212 (77.06%) aligned exactly 1 time 2230536 (13.90%) aligned >1 times 90.96% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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_rmdupse_core] 1646349 / 14596748 = 0.1128 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 09:18:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.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 09:18:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:47: 1000000 INFO @ Tue, 16 Jun 2020 09:18:52: 2000000 INFO @ Tue, 16 Jun 2020 09:18:58: 3000000 INFO @ Tue, 16 Jun 2020 09:19:03: 4000000 INFO @ Tue, 16 Jun 2020 09:19:08: 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 09:19:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.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 09:19:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:14: 6000000 INFO @ Tue, 16 Jun 2020 09:19:18: 1000000 INFO @ Tue, 16 Jun 2020 09:19:21: 7000000 INFO @ Tue, 16 Jun 2020 09:19:24: 2000000 INFO @ Tue, 16 Jun 2020 09:19:27: 8000000 INFO @ Tue, 16 Jun 2020 09:19:31: 3000000 INFO @ Tue, 16 Jun 2020 09:19:34: 9000000 INFO @ Tue, 16 Jun 2020 09:19:37: 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 09:19:40: 10000000 INFO @ Tue, 16 Jun 2020 09:19:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.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 09:19:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:43: 5000000 INFO @ Tue, 16 Jun 2020 09:19:46: 11000000 INFO @ Tue, 16 Jun 2020 09:19:48: 1000000 INFO @ Tue, 16 Jun 2020 09:19:50: 6000000 INFO @ Tue, 16 Jun 2020 09:19:53: 12000000 INFO @ Tue, 16 Jun 2020 09:19:54: 2000000 INFO @ Tue, 16 Jun 2020 09:19:56: 7000000 INFO @ Tue, 16 Jun 2020 09:19:59: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:59: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:59: #1 total tags in treatment: 12950399 INFO @ Tue, 16 Jun 2020 09:19:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:59: #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 09:19:59: #1 tags after filtering in treatment: 12950399 INFO @ Tue, 16 Jun 2020 09:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:00: #2 number of paired peaks: 283 WARNING @ Tue, 16 Jun 2020 09:20:00: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:00: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:20:00: #2 alternative fragment length(s) may be 1,38,593 bps INFO @ Tue, 16 Jun 2020 09:20:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.05_model.r WARNING @ Tue, 16 Jun 2020 09:20:00: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:00: #2 You may need to consider one of the other alternative d(s): 1,38,593 WARNING @ Tue, 16 Jun 2020 09:20:00: #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 09:20:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:00: 3000000 INFO @ Tue, 16 Jun 2020 09:20:02: 8000000 INFO @ Tue, 16 Jun 2020 09:20:07: 4000000 INFO @ Tue, 16 Jun 2020 09:20:09: 9000000 INFO @ Tue, 16 Jun 2020 09:20:13: 5000000 INFO @ Tue, 16 Jun 2020 09:20:15: 10000000 INFO @ Tue, 16 Jun 2020 09:20:19: 6000000 INFO @ Tue, 16 Jun 2020 09:20:21: 11000000 INFO @ Tue, 16 Jun 2020 09:20:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:25: 7000000 INFO @ Tue, 16 Jun 2020 09:20:27: 12000000 INFO @ Tue, 16 Jun 2020 09:20:32: 8000000 INFO @ Tue, 16 Jun 2020 09:20:33: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:33: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:33: #1 total tags in treatment: 12950399 INFO @ Tue, 16 Jun 2020 09:20:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:33: #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 09:20:34: #1 tags after filtering in treatment: 12950399 INFO @ Tue, 16 Jun 2020 09:20:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:35: #2 number of paired peaks: 283 WARNING @ Tue, 16 Jun 2020 09:20:35: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:35: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:20:35: #2 alternative fragment length(s) may be 1,38,593 bps INFO @ Tue, 16 Jun 2020 09:20:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:35: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:35: #2 You may need to consider one of the other alternative d(s): 1,38,593 WARNING @ Tue, 16 Jun 2020 09:20:35: #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 09:20:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (620 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:38: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:44: 10000000 INFO @ Tue, 16 Jun 2020 09:20:50: 11000000 INFO @ Tue, 16 Jun 2020 09:20:55: 12000000 INFO @ Tue, 16 Jun 2020 09:20:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:01: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:21:01: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:21:01: #1 total tags in treatment: 12950399 INFO @ Tue, 16 Jun 2020 09:21:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:01: #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 09:21:01: #1 tags after filtering in treatment: 12950399 INFO @ Tue, 16 Jun 2020 09:21:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:02: #2 number of paired peaks: 283 WARNING @ Tue, 16 Jun 2020 09:21:02: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:02: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:21:02: #2 alternative fragment length(s) may be 1,38,593 bps INFO @ Tue, 16 Jun 2020 09:21:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:02: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:02: #2 You may need to consider one of the other alternative d(s): 1,38,593 WARNING @ Tue, 16 Jun 2020 09:21:02: #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 09:21:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:11: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (338 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494898/SRX494898.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 1 millis CompletedMACS2peakCalling