Job ID = 6366832 SRX = SRX2350731 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:07:53 prefetch.2.10.7: 1) Downloading 'SRR5024040'... 2020-06-15T23:07:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:09:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:09:34 prefetch.2.10.7: 1) 'SRR5024040' was downloaded successfully Read 13822311 spots for SRR5024040/SRR5024040.sra Written 13822311 spots for SRR5024040/SRR5024040.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: 00:03:20 13822311 reads; of these: 13822311 (100.00%) were unpaired; of these: 630354 (4.56%) aligned 0 times 10466537 (75.72%) aligned exactly 1 time 2725420 (19.72%) aligned >1 times 95.44% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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_rmdupse_core] 1657152 / 13191957 = 0.1256 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 08:17:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.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 08:17:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:26: 1000000 INFO @ Tue, 16 Jun 2020 08:17:32: 2000000 INFO @ Tue, 16 Jun 2020 08:17:38: 3000000 INFO @ Tue, 16 Jun 2020 08:17:44: 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 @ Tue, 16 Jun 2020 08:17:50: 5000000 INFO @ Tue, 16 Jun 2020 08:17:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.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 08:17:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:57: 6000000 INFO @ Tue, 16 Jun 2020 08:17:57: 1000000 INFO @ Tue, 16 Jun 2020 08:18:04: 7000000 INFO @ Tue, 16 Jun 2020 08:18:05: 2000000 INFO @ Tue, 16 Jun 2020 08:18:11: 8000000 INFO @ Tue, 16 Jun 2020 08:18:12: 3000000 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 08:18:18: 9000000 INFO @ Tue, 16 Jun 2020 08:18:20: 4000000 INFO @ Tue, 16 Jun 2020 08:18:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.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 08:18:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:26: 10000000 INFO @ Tue, 16 Jun 2020 08:18:27: 5000000 INFO @ Tue, 16 Jun 2020 08:18:28: 1000000 INFO @ Tue, 16 Jun 2020 08:18:33: 11000000 INFO @ Tue, 16 Jun 2020 08:18:35: 6000000 INFO @ Tue, 16 Jun 2020 08:18:35: 2000000 INFO @ Tue, 16 Jun 2020 08:18:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:18:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:18:37: #1 total tags in treatment: 11534805 INFO @ Tue, 16 Jun 2020 08:18:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:37: #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 08:18:37: #1 tags after filtering in treatment: 11534805 INFO @ Tue, 16 Jun 2020 08:18:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:38: #2 number of paired peaks: 329 WARNING @ Tue, 16 Jun 2020 08:18:38: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:38: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 08:18:38: #2 alternative fragment length(s) may be 2,39,555 bps INFO @ Tue, 16 Jun 2020 08:18:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.05_model.r WARNING @ Tue, 16 Jun 2020 08:18:38: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:38: #2 You may need to consider one of the other alternative d(s): 2,39,555 WARNING @ Tue, 16 Jun 2020 08:18:38: #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 08:18:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:42: 7000000 INFO @ Tue, 16 Jun 2020 08:18:43: 3000000 INFO @ Tue, 16 Jun 2020 08:18:50: 8000000 INFO @ Tue, 16 Jun 2020 08:18:50: 4000000 INFO @ Tue, 16 Jun 2020 08:18:57: 9000000 INFO @ Tue, 16 Jun 2020 08:18:58: 5000000 INFO @ Tue, 16 Jun 2020 08:19:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:04: 10000000 INFO @ Tue, 16 Jun 2020 08:19:06: 6000000 INFO @ Tue, 16 Jun 2020 08:19:12: 11000000 INFO @ Tue, 16 Jun 2020 08:19:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.05_summits.bed INFO @ Tue, 16 Jun 2020 08:19:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (741 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:19:13: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:19:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:19:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:19:16: #1 total tags in treatment: 11534805 INFO @ Tue, 16 Jun 2020 08:19:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:16: #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 08:19:16: #1 tags after filtering in treatment: 11534805 INFO @ Tue, 16 Jun 2020 08:19:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:17: #2 number of paired peaks: 329 WARNING @ Tue, 16 Jun 2020 08:19:17: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:17: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 08:19:17: #2 alternative fragment length(s) may be 2,39,555 bps INFO @ Tue, 16 Jun 2020 08:19:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.10_model.r WARNING @ Tue, 16 Jun 2020 08:19:17: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:17: #2 You may need to consider one of the other alternative d(s): 2,39,555 WARNING @ Tue, 16 Jun 2020 08:19:17: #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 08:19:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:20: 8000000 INFO @ Tue, 16 Jun 2020 08:19:27: 9000000 INFO @ Tue, 16 Jun 2020 08:19:34: 10000000 INFO @ Tue, 16 Jun 2020 08:19:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:41: 11000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:19:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:19:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:19:45: #1 total tags in treatment: 11534805 INFO @ Tue, 16 Jun 2020 08:19:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:45: #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 08:19:45: #1 tags after filtering in treatment: 11534805 INFO @ Tue, 16 Jun 2020 08:19:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:46: #2 number of paired peaks: 329 WARNING @ Tue, 16 Jun 2020 08:19:46: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:46: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 08:19:46: #2 alternative fragment length(s) may be 2,39,555 bps INFO @ Tue, 16 Jun 2020 08:19:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.20_model.r WARNING @ Tue, 16 Jun 2020 08:19:46: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:46: #2 You may need to consider one of the other alternative d(s): 2,39,555 WARNING @ Tue, 16 Jun 2020 08:19:46: #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 08:19:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.10_summits.bed INFO @ Tue, 16 Jun 2020 08:19:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (414 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350731/SRX2350731.20_summits.bed INFO @ Tue, 16 Jun 2020 08:20:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (142 records, 4 fields): 2 millis CompletedMACS2peakCalling