Job ID = 6368122 SRX = SRX466585 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:00:35 prefetch.2.10.7: 1) Downloading 'SRR1163651'... 2020-06-16T00:00:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:02:49 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:02:49 prefetch.2.10.7: 1) 'SRR1163651' was downloaded successfully Read 18755646 spots for SRR1163651/SRR1163651.sra Written 18755646 spots for SRR1163651/SRR1163651.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: 00:03:49 18755646 reads; of these: 18755646 (100.00%) were unpaired; of these: 183681 (0.98%) aligned 0 times 15172359 (80.89%) aligned exactly 1 time 3399606 (18.13%) aligned >1 times 99.02% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 4539916 / 18571965 = 0.2444 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 09:12:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.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 09:12:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:17: 1000000 INFO @ Tue, 16 Jun 2020 09:12:22: 2000000 INFO @ Tue, 16 Jun 2020 09:12:28: 3000000 INFO @ Tue, 16 Jun 2020 09:12:33: 4000000 INFO @ Tue, 16 Jun 2020 09:12:38: 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 09:12:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.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 09:12:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:43: 6000000 INFO @ Tue, 16 Jun 2020 09:12:48: 1000000 INFO @ Tue, 16 Jun 2020 09:12:49: 7000000 INFO @ Tue, 16 Jun 2020 09:12:53: 2000000 INFO @ Tue, 16 Jun 2020 09:12:55: 8000000 INFO @ Tue, 16 Jun 2020 09:12:59: 3000000 INFO @ Tue, 16 Jun 2020 09:13:00: 9000000 INFO @ Tue, 16 Jun 2020 09:13:04: 4000000 INFO @ Tue, 16 Jun 2020 09:13:06: 10000000 INFO @ Tue, 16 Jun 2020 09:13:10: 5000000 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 09:13:11: 11000000 INFO @ Tue, 16 Jun 2020 09:13:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.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 09:13:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:15: 6000000 INFO @ Tue, 16 Jun 2020 09:13:17: 12000000 INFO @ Tue, 16 Jun 2020 09:13:18: 1000000 INFO @ Tue, 16 Jun 2020 09:13:21: 7000000 INFO @ Tue, 16 Jun 2020 09:13:23: 13000000 INFO @ Tue, 16 Jun 2020 09:13:24: 2000000 INFO @ Tue, 16 Jun 2020 09:13:27: 8000000 INFO @ Tue, 16 Jun 2020 09:13:29: 14000000 INFO @ Tue, 16 Jun 2020 09:13:29: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:13:29: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:13:29: #1 total tags in treatment: 14032049 INFO @ Tue, 16 Jun 2020 09:13:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:29: #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 09:13:29: #1 tags after filtering in treatment: 14032049 INFO @ Tue, 16 Jun 2020 09:13:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:29: 3000000 INFO @ Tue, 16 Jun 2020 09:13:30: #2 number of paired peaks: 433 WARNING @ Tue, 16 Jun 2020 09:13:30: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:30: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:13:30: #2 alternative fragment length(s) may be 1,38 bps INFO @ Tue, 16 Jun 2020 09:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.05_model.r WARNING @ Tue, 16 Jun 2020 09:13:30: #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 09:13:30: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Tue, 16 Jun 2020 09:13:30: #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 09:13:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:33: 9000000 INFO @ Tue, 16 Jun 2020 09:13:35: 4000000 INFO @ Tue, 16 Jun 2020 09:13:38: 10000000 INFO @ Tue, 16 Jun 2020 09:13:41: 5000000 INFO @ Tue, 16 Jun 2020 09:13:44: 11000000 INFO @ Tue, 16 Jun 2020 09:13:46: 6000000 INFO @ Tue, 16 Jun 2020 09:13:49: 12000000 INFO @ Tue, 16 Jun 2020 09:13:52: 7000000 INFO @ Tue, 16 Jun 2020 09:13:55: 13000000 INFO @ Tue, 16 Jun 2020 09:13:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:58: 8000000 INFO @ Tue, 16 Jun 2020 09:14:01: 14000000 INFO @ Tue, 16 Jun 2020 09:14:01: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:14:01: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:14:01: #1 total tags in treatment: 14032049 INFO @ Tue, 16 Jun 2020 09:14:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:01: #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 09:14:01: #1 tags after filtering in treatment: 14032049 INFO @ Tue, 16 Jun 2020 09:14:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:02: #2 number of paired peaks: 433 WARNING @ Tue, 16 Jun 2020 09:14:02: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:02: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:14:02: #2 alternative fragment length(s) may be 1,38 bps INFO @ Tue, 16 Jun 2020 09:14:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.10_model.r WARNING @ Tue, 16 Jun 2020 09:14:02: #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 09:14:02: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Tue, 16 Jun 2020 09:14:02: #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 09:14:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:04: 9000000 INFO @ Tue, 16 Jun 2020 09:14:10: 10000000 INFO @ Tue, 16 Jun 2020 09:14:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.05_summits.bed INFO @ Tue, 16 Jun 2020 09:14:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1242 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:15: 11000000 INFO @ Tue, 16 Jun 2020 09:14:21: 12000000 INFO @ Tue, 16 Jun 2020 09:14:27: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:14:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:32: 14000000 INFO @ Tue, 16 Jun 2020 09:14:33: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:14:33: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:14:33: #1 total tags in treatment: 14032049 INFO @ Tue, 16 Jun 2020 09:14:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:33: #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 09:14:33: #1 tags after filtering in treatment: 14032049 INFO @ Tue, 16 Jun 2020 09:14:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:34: #2 number of paired peaks: 433 WARNING @ Tue, 16 Jun 2020 09:14:34: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:34: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:14:34: #2 alternative fragment length(s) may be 1,38 bps INFO @ Tue, 16 Jun 2020 09:14:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.20_model.r WARNING @ Tue, 16 Jun 2020 09:14:34: #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 09:14:34: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Tue, 16 Jun 2020 09:14:34: #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 09:14:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.10_summits.bed INFO @ Tue, 16 Jun 2020 09:14:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (531 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:15:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466585/SRX466585.20_summits.bed INFO @ Tue, 16 Jun 2020 09:15:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (177 records, 4 fields): 1 millis CompletedMACS2peakCalling