Job ID = 6367702 SRX = SRX395526 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:20 prefetch.2.10.7: 1) Downloading 'SRR1054252'... 2020-06-15T23:34:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:19 prefetch.2.10.7: 'SRR1054252' is valid 2020-06-15T23:35:19 prefetch.2.10.7: 1) 'SRR1054252' was downloaded successfully Read 8574104 spots for SRR1054252/SRR1054252.sra Written 8574104 spots for SRR1054252/SRR1054252.sra 2020-06-15T23:35:52 prefetch.2.10.7: 1) Downloading 'SRR1054253'... 2020-06-15T23:35:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:30 prefetch.2.10.7: 'SRR1054253' is valid 2020-06-15T23:36:30 prefetch.2.10.7: 1) 'SRR1054253' was downloaded successfully Read 5029554 spots for SRR1054253/SRR1054253.sra Written 5029554 spots for SRR1054253/SRR1054253.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: 00:01:58 13603658 reads; of these: 13603658 (100.00%) were unpaired; of these: 92026 (0.68%) aligned 0 times 11333599 (83.31%) aligned exactly 1 time 2178033 (16.01%) aligned >1 times 99.32% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 1675136 / 13511632 = 0.1240 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 08:41:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.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 08:41:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:44: 1000000 INFO @ Tue, 16 Jun 2020 08:41:49: 2000000 INFO @ Tue, 16 Jun 2020 08:41:54: 3000000 INFO @ Tue, 16 Jun 2020 08:42:00: 4000000 INFO @ Tue, 16 Jun 2020 08:42:05: 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 08:42:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.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 08:42:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:10: 6000000 INFO @ Tue, 16 Jun 2020 08:42:15: 1000000 INFO @ Tue, 16 Jun 2020 08:42:16: 7000000 INFO @ Tue, 16 Jun 2020 08:42:20: 2000000 INFO @ Tue, 16 Jun 2020 08:42:21: 8000000 INFO @ Tue, 16 Jun 2020 08:42:26: 3000000 INFO @ Tue, 16 Jun 2020 08:42:27: 9000000 INFO @ Tue, 16 Jun 2020 08:42:31: 4000000 INFO @ Tue, 16 Jun 2020 08:42:32: 10000000 INFO @ Tue, 16 Jun 2020 08:42:37: 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 08:42:38: 11000000 INFO @ Tue, 16 Jun 2020 08:42:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.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 08:42:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:42:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:42:43: #1 total tags in treatment: 11836496 INFO @ Tue, 16 Jun 2020 08:42:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:43: #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 08:42:43: 6000000 INFO @ Tue, 16 Jun 2020 08:42:43: #1 tags after filtering in treatment: 11836496 INFO @ Tue, 16 Jun 2020 08:42:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:43: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 08:42:43: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:44: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:42:44: #2 alternative fragment length(s) may be 2,31,557,582 bps INFO @ Tue, 16 Jun 2020 08:42:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.05_model.r WARNING @ Tue, 16 Jun 2020 08:42:44: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:44: #2 You may need to consider one of the other alternative d(s): 2,31,557,582 WARNING @ Tue, 16 Jun 2020 08:42:44: #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 08:42:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:45: 1000000 INFO @ Tue, 16 Jun 2020 08:42:48: 7000000 INFO @ Tue, 16 Jun 2020 08:42:50: 2000000 INFO @ Tue, 16 Jun 2020 08:42:54: 8000000 INFO @ Tue, 16 Jun 2020 08:42:56: 3000000 INFO @ Tue, 16 Jun 2020 08:42:59: 9000000 INFO @ Tue, 16 Jun 2020 08:43:01: 4000000 INFO @ Tue, 16 Jun 2020 08:43:05: 10000000 INFO @ Tue, 16 Jun 2020 08:43:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:07: 5000000 INFO @ Tue, 16 Jun 2020 08:43:10: 11000000 INFO @ Tue, 16 Jun 2020 08:43:13: 6000000 INFO @ Tue, 16 Jun 2020 08:43:15: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:43:15: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:43:15: #1 total tags in treatment: 11836496 INFO @ Tue, 16 Jun 2020 08:43:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:15: #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 08:43:15: #1 tags after filtering in treatment: 11836496 INFO @ Tue, 16 Jun 2020 08:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.05_summits.bed INFO @ Tue, 16 Jun 2020 08:43:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:43:16: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 08:43:16: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 08:43:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:16: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:43:16: #2 alternative fragment length(s) may be 2,31,557,582 bps INFO @ Tue, 16 Jun 2020 08:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.10_model.r WARNING @ Tue, 16 Jun 2020 08:43:16: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:16: #2 You may need to consider one of the other alternative d(s): 2,31,557,582 WARNING @ Tue, 16 Jun 2020 08:43:16: #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 08:43:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:43:18: 7000000 INFO @ Tue, 16 Jun 2020 08:43:23: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:43:28: 9000000 INFO @ Tue, 16 Jun 2020 08:43:33: 10000000 INFO @ Tue, 16 Jun 2020 08:43:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:38: 11000000 INFO @ Tue, 16 Jun 2020 08:43:42: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:43:42: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:43:42: #1 total tags in treatment: 11836496 INFO @ Tue, 16 Jun 2020 08:43:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:42: #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 08:43:42: #1 tags after filtering in treatment: 11836496 INFO @ Tue, 16 Jun 2020 08:43:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:43: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 08:43:43: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 08:43:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:43: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:43:43: #2 alternative fragment length(s) may be 2,31,557,582 bps INFO @ Tue, 16 Jun 2020 08:43:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.20_model.r WARNING @ Tue, 16 Jun 2020 08:43:43: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:43: #2 You may need to consider one of the other alternative d(s): 2,31,557,582 WARNING @ Tue, 16 Jun 2020 08:43:43: #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 08:43:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:43:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.10_summits.bed INFO @ Tue, 16 Jun 2020 08:43:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:44:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395526/SRX395526.20_summits.bed INFO @ Tue, 16 Jun 2020 08:44:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 1 millis CompletedMACS2peakCalling