Job ID = 6626529 SRX = SRX7262221 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:34 17986801 reads; of these: 17986801 (100.00%) were unpaired; of these: 3685572 (20.49%) aligned 0 times 11136470 (61.91%) aligned exactly 1 time 3164759 (17.59%) aligned >1 times 79.51% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 2880629 / 14301229 = 0.2014 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 07:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.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 07:27:39: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:27:39: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:27:44: 1000000 INFO @ Tue, 14 Jul 2020 07:27:49: 2000000 INFO @ Tue, 14 Jul 2020 07:27:54: 3000000 INFO @ Tue, 14 Jul 2020 07:27:59: 4000000 INFO @ Tue, 14 Jul 2020 07:28:04: 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 07:28:08: 6000000 INFO @ Tue, 14 Jul 2020 07:28:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.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 07:28:09: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:09: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:13: 7000000 INFO @ Tue, 14 Jul 2020 07:28:14: 1000000 INFO @ Tue, 14 Jul 2020 07:28:18: 8000000 INFO @ Tue, 14 Jul 2020 07:28:19: 2000000 INFO @ Tue, 14 Jul 2020 07:28:23: 9000000 INFO @ Tue, 14 Jul 2020 07:28:24: 3000000 INFO @ Tue, 14 Jul 2020 07:28:27: 10000000 INFO @ Tue, 14 Jul 2020 07:28:29: 4000000 INFO @ Tue, 14 Jul 2020 07:28:32: 11000000 INFO @ Tue, 14 Jul 2020 07:28:34: 5000000 INFO @ Tue, 14 Jul 2020 07:28:34: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:28:34: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:28:34: #1 total tags in treatment: 11420600 INFO @ Tue, 14 Jul 2020 07:28:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:28:34: #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 07:28:34: #1 tags after filtering in treatment: 11420600 INFO @ Tue, 14 Jul 2020 07:28:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:28:34: #1 finished! INFO @ Tue, 14 Jul 2020 07:28:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:28:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:28:35: #2 number of paired peaks: 482 WARNING @ Tue, 14 Jul 2020 07:28:35: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Tue, 14 Jul 2020 07:28:35: start model_add_line... INFO @ Tue, 14 Jul 2020 07:28:35: start X-correlation... INFO @ Tue, 14 Jul 2020 07:28:35: end of X-cor INFO @ Tue, 14 Jul 2020 07:28:35: #2 finished! INFO @ Tue, 14 Jul 2020 07:28:35: #2 predicted fragment length is 41 bps INFO @ Tue, 14 Jul 2020 07:28:35: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 14 Jul 2020 07:28:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.05_model.r WARNING @ Tue, 14 Jul 2020 07:28:35: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:28:35: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 14 Jul 2020 07:28:35: #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 07:28:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:28:35: #3 Pre-compute pvalue-qvalue table... 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 07:28:38: 6000000 INFO @ Tue, 14 Jul 2020 07:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.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 07:28:39: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:39: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:43: 7000000 INFO @ Tue, 14 Jul 2020 07:28:44: 1000000 INFO @ Tue, 14 Jul 2020 07:28:48: 8000000 INFO @ Tue, 14 Jul 2020 07:28:49: 2000000 INFO @ Tue, 14 Jul 2020 07:28:53: 9000000 INFO @ Tue, 14 Jul 2020 07:28:55: 3000000 INFO @ Tue, 14 Jul 2020 07:28:55: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:28:58: 10000000 INFO @ Tue, 14 Jul 2020 07:28:59: 4000000 INFO @ Tue, 14 Jul 2020 07:29:02: 11000000 INFO @ Tue, 14 Jul 2020 07:29:04: 5000000 INFO @ Tue, 14 Jul 2020 07:29:04: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:29:04: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:29:04: #1 total tags in treatment: 11420600 INFO @ Tue, 14 Jul 2020 07:29:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:29:04: #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 07:29:05: #1 tags after filtering in treatment: 11420600 INFO @ Tue, 14 Jul 2020 07:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:29:05: #1 finished! INFO @ Tue, 14 Jul 2020 07:29:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:29:05: #2 number of paired peaks: 482 WARNING @ Tue, 14 Jul 2020 07:29:05: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Tue, 14 Jul 2020 07:29:05: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.05_summits.bed INFO @ Tue, 14 Jul 2020 07:29:05: Done! INFO @ Tue, 14 Jul 2020 07:29:05: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:05: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:05: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:05: #2 predicted fragment length is 41 bps INFO @ Tue, 14 Jul 2020 07:29:05: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 14 Jul 2020 07:29:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.10_model.r WARNING @ Tue, 14 Jul 2020 07:29:05: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:29:05: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 14 Jul 2020 07:29:05: #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 07:29:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:05: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (759 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:29:09: 6000000 INFO @ Tue, 14 Jul 2020 07:29:14: 7000000 INFO @ Tue, 14 Jul 2020 07:29:18: 8000000 INFO @ Tue, 14 Jul 2020 07:29:23: 9000000 INFO @ Tue, 14 Jul 2020 07:29:27: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:29:28: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:29:32: 11000000 INFO @ Tue, 14 Jul 2020 07:29:34: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:29:34: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:29:34: #1 total tags in treatment: 11420600 INFO @ Tue, 14 Jul 2020 07:29:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:29:34: #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 07:29:35: #1 tags after filtering in treatment: 11420600 INFO @ Tue, 14 Jul 2020 07:29:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:29:35: #1 finished! INFO @ Tue, 14 Jul 2020 07:29:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:29:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:29:35: #2 number of paired peaks: 482 WARNING @ Tue, 14 Jul 2020 07:29:35: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Tue, 14 Jul 2020 07:29:35: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:35: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:36: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:36: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:36: #2 predicted fragment length is 41 bps INFO @ Tue, 14 Jul 2020 07:29:36: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 14 Jul 2020 07:29:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.20_model.r WARNING @ Tue, 14 Jul 2020 07:29:36: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:29:36: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 14 Jul 2020 07:29:36: #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 07:29:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:29:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:29:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:29:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.10_summits.bed INFO @ Tue, 14 Jul 2020 07:29:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (429 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:29:57: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:30:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262221/SRX7262221.20_summits.bed INFO @ Tue, 14 Jul 2020 07:30:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (151 records, 4 fields): 15 millis CompletedMACS2peakCalling