Job ID = 6626460 SRX = SRX7262218 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:01:46 8695122 reads; of these: 8695122 (100.00%) were unpaired; of these: 1039171 (11.95%) aligned 0 times 6016269 (69.19%) aligned exactly 1 time 1639682 (18.86%) aligned >1 times 88.05% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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] 1431366 / 7655951 = 0.1870 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, 14 Jul 2020 07:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.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, 14 Jul 2020 07:07:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:07:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:07:24: 1000000 INFO @ Tue, 14 Jul 2020 07:07:29: 2000000 INFO @ Tue, 14 Jul 2020 07:07:34: 3000000 INFO @ Tue, 14 Jul 2020 07:07:39: 4000000 INFO @ Tue, 14 Jul 2020 07:07:45: 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, 14 Jul 2020 07:07:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.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, 14 Jul 2020 07:07:48: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:07:48: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:07:50: 6000000 INFO @ Tue, 14 Jul 2020 07:07:51: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:51: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:51: #1 total tags in treatment: 6224585 INFO @ Tue, 14 Jul 2020 07:07:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:07:51: #1 tags after filtering in treatment: 6224585 INFO @ Tue, 14 Jul 2020 07:07:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:51: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:52: #2 number of paired peaks: 474 WARNING @ Tue, 14 Jul 2020 07:07:52: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:52: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:52: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:52: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:52: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:52: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:07:52: #2 alternative fragment length(s) may be 4,50,535,545 bps INFO @ Tue, 14 Jul 2020 07:07:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.05_model.r WARNING @ Tue, 14 Jul 2020 07:07:52: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:07:52: #2 You may need to consider one of the other alternative d(s): 4,50,535,545 WARNING @ Tue, 14 Jul 2020 07:07:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:07:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:07:54: 1000000 INFO @ Tue, 14 Jul 2020 07:07:59: 2000000 INFO @ Tue, 14 Jul 2020 07:08:04: 3000000 INFO @ Tue, 14 Jul 2020 07:08:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:08:09: 4000000 INFO @ Tue, 14 Jul 2020 07:08:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:08:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:08:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.05_summits.bed INFO @ Tue, 14 Jul 2020 07:08:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (589 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:08:14: 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, 14 Jul 2020 07:08:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.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, 14 Jul 2020 07:08:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:08:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:08:20: 6000000 INFO @ Tue, 14 Jul 2020 07:08:21: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:08:21: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:08:21: #1 total tags in treatment: 6224585 INFO @ Tue, 14 Jul 2020 07:08:21: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:08:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:08:21: #1 tags after filtering in treatment: 6224585 INFO @ Tue, 14 Jul 2020 07:08:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:08:21: #1 finished! INFO @ Tue, 14 Jul 2020 07:08:21: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:08:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:08:21: #2 number of paired peaks: 474 WARNING @ Tue, 14 Jul 2020 07:08:21: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 14 Jul 2020 07:08:21: start model_add_line... INFO @ Tue, 14 Jul 2020 07:08:21: start X-correlation... INFO @ Tue, 14 Jul 2020 07:08:21: end of X-cor INFO @ Tue, 14 Jul 2020 07:08:21: #2 finished! INFO @ Tue, 14 Jul 2020 07:08:21: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:08:21: #2 alternative fragment length(s) may be 4,50,535,545 bps INFO @ Tue, 14 Jul 2020 07:08:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.10_model.r WARNING @ Tue, 14 Jul 2020 07:08:21: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:08:21: #2 You may need to consider one of the other alternative d(s): 4,50,535,545 WARNING @ Tue, 14 Jul 2020 07:08:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:08:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:08:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:08:24: 1000000 INFO @ Tue, 14 Jul 2020 07:08:29: 2000000 INFO @ Tue, 14 Jul 2020 07:08:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:08:34: 3000000 INFO @ Tue, 14 Jul 2020 07:08:40: 4000000 INFO @ Tue, 14 Jul 2020 07:08:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:08:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:08:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.10_summits.bed INFO @ Tue, 14 Jul 2020 07:08:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (389 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:08:45: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:08:50: 6000000 INFO @ Tue, 14 Jul 2020 07:08:51: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:08:51: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:08:51: #1 total tags in treatment: 6224585 INFO @ Tue, 14 Jul 2020 07:08:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:08:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:08:51: #1 tags after filtering in treatment: 6224585 INFO @ Tue, 14 Jul 2020 07:08:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:08:51: #1 finished! INFO @ Tue, 14 Jul 2020 07:08:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:08:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:08:52: #2 number of paired peaks: 474 WARNING @ Tue, 14 Jul 2020 07:08:52: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 14 Jul 2020 07:08:52: start model_add_line... INFO @ Tue, 14 Jul 2020 07:08:52: start X-correlation... INFO @ Tue, 14 Jul 2020 07:08:52: end of X-cor INFO @ Tue, 14 Jul 2020 07:08:52: #2 finished! INFO @ Tue, 14 Jul 2020 07:08:52: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:08:52: #2 alternative fragment length(s) may be 4,50,535,545 bps INFO @ Tue, 14 Jul 2020 07:08:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.20_model.r WARNING @ Tue, 14 Jul 2020 07:08:52: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:08:52: #2 You may need to consider one of the other alternative d(s): 4,50,535,545 WARNING @ Tue, 14 Jul 2020 07:08:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:08:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:08:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:09:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:09:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:09:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262218/SRX7262218.20_summits.bed INFO @ Tue, 14 Jul 2020 07:09:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (158 records, 4 fields): 29 millis CompletedMACS2peakCalling