Job ID = 6367024 SRX = SRX2710285 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:12:46 prefetch.2.10.7: 1) Downloading 'SRR5418739'... 2020-06-15T23:12:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:15:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:15:21 prefetch.2.10.7: 1) 'SRR5418739' was downloaded successfully Read 27553640 spots for SRR5418739/SRR5418739.sra Written 27553640 spots for SRR5418739/SRR5418739.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: 00:06:33 27553640 reads; of these: 27553640 (100.00%) were unpaired; of these: 5961471 (21.64%) aligned 0 times 12666813 (45.97%) aligned exactly 1 time 8925356 (32.39%) aligned >1 times 78.36% overall alignment rate Time searching: 00:06:33 Overall time: 00:06:33 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 12 files... [bam_rmdupse_core] 8928248 / 21592169 = 0.4135 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 08:28:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.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 08:28:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:19: 1000000 INFO @ Tue, 16 Jun 2020 08:28:25: 2000000 INFO @ Tue, 16 Jun 2020 08:28:30: 3000000 INFO @ Tue, 16 Jun 2020 08:28:36: 4000000 INFO @ Tue, 16 Jun 2020 08:28:41: 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 08:28:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.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 08:28:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:47: 6000000 INFO @ Tue, 16 Jun 2020 08:28:52: 1000000 INFO @ Tue, 16 Jun 2020 08:28:53: 7000000 INFO @ Tue, 16 Jun 2020 08:28:59: 2000000 INFO @ Tue, 16 Jun 2020 08:29:00: 8000000 INFO @ Tue, 16 Jun 2020 08:29:06: 9000000 INFO @ Tue, 16 Jun 2020 08:29:06: 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 08:29:12: 10000000 INFO @ Tue, 16 Jun 2020 08:29:13: 4000000 INFO @ Tue, 16 Jun 2020 08:29:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.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 08:29:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:18: 11000000 INFO @ Tue, 16 Jun 2020 08:29:20: 1000000 INFO @ Tue, 16 Jun 2020 08:29:20: 5000000 INFO @ Tue, 16 Jun 2020 08:29:25: 12000000 INFO @ Tue, 16 Jun 2020 08:29:26: 2000000 INFO @ Tue, 16 Jun 2020 08:29:28: 6000000 INFO @ Tue, 16 Jun 2020 08:29:29: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:29:29: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:29:29: #1 total tags in treatment: 12663921 INFO @ Tue, 16 Jun 2020 08:29:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:29: #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 08:29:29: #1 tags after filtering in treatment: 12663921 INFO @ Tue, 16 Jun 2020 08:29:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:30: #2 number of paired peaks: 867 WARNING @ Tue, 16 Jun 2020 08:29:30: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Tue, 16 Jun 2020 08:29:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:30: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 08:29:30: #2 alternative fragment length(s) may be 2,63 bps INFO @ Tue, 16 Jun 2020 08:29:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.05_model.r WARNING @ Tue, 16 Jun 2020 08:29:30: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:29:30: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Tue, 16 Jun 2020 08:29:30: #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 08:29:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:32: 3000000 INFO @ Tue, 16 Jun 2020 08:29:35: 7000000 INFO @ Tue, 16 Jun 2020 08:29:39: 4000000 INFO @ Tue, 16 Jun 2020 08:29:42: 8000000 INFO @ Tue, 16 Jun 2020 08:29:45: 5000000 INFO @ Tue, 16 Jun 2020 08:29:49: 9000000 INFO @ Tue, 16 Jun 2020 08:29:51: 6000000 INFO @ Tue, 16 Jun 2020 08:29:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:56: 10000000 INFO @ Tue, 16 Jun 2020 08:29:57: 7000000 INFO @ Tue, 16 Jun 2020 08:30:03: 11000000 INFO @ Tue, 16 Jun 2020 08:30:03: 8000000 INFO @ Tue, 16 Jun 2020 08:30:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.05_summits.bed INFO @ Tue, 16 Jun 2020 08:30:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7914 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:30:10: 12000000 INFO @ Tue, 16 Jun 2020 08:30:10: 9000000 INFO @ Tue, 16 Jun 2020 08:30:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:30:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:30:14: #1 total tags in treatment: 12663921 INFO @ Tue, 16 Jun 2020 08:30:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:14: #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 08:30:14: #1 tags after filtering in treatment: 12663921 INFO @ Tue, 16 Jun 2020 08:30:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:15: #2 number of paired peaks: 867 WARNING @ Tue, 16 Jun 2020 08:30:15: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:15: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 08:30:15: #2 alternative fragment length(s) may be 2,63 bps INFO @ Tue, 16 Jun 2020 08:30:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.10_model.r WARNING @ Tue, 16 Jun 2020 08:30:15: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:15: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Tue, 16 Jun 2020 08:30:15: #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 08:30:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:16: 10000000 INFO @ Tue, 16 Jun 2020 08:30:22: 11000000 INFO @ Tue, 16 Jun 2020 08:30:27: 12000000 INFO @ Tue, 16 Jun 2020 08:30:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:30:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:30:31: #1 total tags in treatment: 12663921 INFO @ Tue, 16 Jun 2020 08:30:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:31: #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 08:30:31: #1 tags after filtering in treatment: 12663921 INFO @ Tue, 16 Jun 2020 08:30:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:32: #2 number of paired peaks: 867 WARNING @ Tue, 16 Jun 2020 08:30:32: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:32: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 08:30:32: #2 alternative fragment length(s) may be 2,63 bps INFO @ Tue, 16 Jun 2020 08:30:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.20_model.r WARNING @ Tue, 16 Jun 2020 08:30:32: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:32: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Tue, 16 Jun 2020 08:30:32: #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 08:30:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:30:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.10_summits.bed INFO @ Tue, 16 Jun 2020 08:30:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3247 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:30:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710285/SRX2710285.20_summits.bed INFO @ Tue, 16 Jun 2020 08:31:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (846 records, 4 fields): 3 millis CompletedMACS2peakCalling