Job ID = 10166171 SRX = SRX8331156 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: 00:29:14 83266129 reads; of these: 83266129 (100.00%) were unpaired; of these: 759709 (0.91%) aligned 0 times 69563809 (83.54%) aligned exactly 1 time 12942611 (15.54%) aligned >1 times 99.09% overall alignment rate Time searching: 00:29:14 Overall time: 00:29:14 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 36 files... [bam_rmdupse_core] 69310044 / 82506420 = 0.8401 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 @ Thu, 08 Oct 2020 21:18:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.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 @ Thu, 08 Oct 2020 21:18:07: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:18:07: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:18:13: 1000000 INFO @ Thu, 08 Oct 2020 21:18:19: 2000000 INFO @ Thu, 08 Oct 2020 21:18:25: 3000000 INFO @ Thu, 08 Oct 2020 21:18:31: 4000000 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 @ Thu, 08 Oct 2020 21:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.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 @ Thu, 08 Oct 2020 21:18:37: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:18:37: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:18:38: 5000000 INFO @ Thu, 08 Oct 2020 21:18:44: 1000000 INFO @ Thu, 08 Oct 2020 21:18:44: 6000000 INFO @ Thu, 08 Oct 2020 21:18:50: 2000000 INFO @ Thu, 08 Oct 2020 21:18:51: 7000000 INFO @ Thu, 08 Oct 2020 21:18:57: 3000000 INFO @ Thu, 08 Oct 2020 21:18:58: 8000000 INFO @ Thu, 08 Oct 2020 21:19:04: 4000000 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 @ Thu, 08 Oct 2020 21:19:05: 9000000 INFO @ Thu, 08 Oct 2020 21:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.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 @ Thu, 08 Oct 2020 21:19:07: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:19:07: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:19:11: 5000000 INFO @ Thu, 08 Oct 2020 21:19:12: 10000000 INFO @ Thu, 08 Oct 2020 21:19:14: 1000000 INFO @ Thu, 08 Oct 2020 21:19:18: 6000000 INFO @ Thu, 08 Oct 2020 21:19:19: 11000000 INFO @ Thu, 08 Oct 2020 21:19:21: 2000000 INFO @ Thu, 08 Oct 2020 21:19:25: 7000000 INFO @ Thu, 08 Oct 2020 21:19:26: 12000000 INFO @ Thu, 08 Oct 2020 21:19:28: 3000000 INFO @ Thu, 08 Oct 2020 21:19:32: 8000000 INFO @ Thu, 08 Oct 2020 21:19:33: 13000000 INFO @ Thu, 08 Oct 2020 21:19:34: #1 tag size is determined as 64 bps INFO @ Thu, 08 Oct 2020 21:19:34: #1 tag size = 64 INFO @ Thu, 08 Oct 2020 21:19:34: #1 total tags in treatment: 13196376 INFO @ Thu, 08 Oct 2020 21:19:34: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:19:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:19:34: #1 tags after filtering in treatment: 13196376 INFO @ Thu, 08 Oct 2020 21:19:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:19:34: #1 finished! INFO @ Thu, 08 Oct 2020 21:19:34: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:19:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:19:35: 4000000 INFO @ Thu, 08 Oct 2020 21:19:35: #2 number of paired peaks: 738 WARNING @ Thu, 08 Oct 2020 21:19:35: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Thu, 08 Oct 2020 21:19:35: start model_add_line... INFO @ Thu, 08 Oct 2020 21:19:35: start X-correlation... INFO @ Thu, 08 Oct 2020 21:19:35: end of X-cor INFO @ Thu, 08 Oct 2020 21:19:35: #2 finished! INFO @ Thu, 08 Oct 2020 21:19:35: #2 predicted fragment length is 54 bps INFO @ Thu, 08 Oct 2020 21:19:35: #2 alternative fragment length(s) may be 2,54 bps INFO @ Thu, 08 Oct 2020 21:19:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.05_model.r WARNING @ Thu, 08 Oct 2020 21:19:35: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:19:35: #2 You may need to consider one of the other alternative d(s): 2,54 WARNING @ Thu, 08 Oct 2020 21:19:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:19:35: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:19:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:19:39: 9000000 INFO @ Thu, 08 Oct 2020 21:19:42: 5000000 INFO @ Thu, 08 Oct 2020 21:19:46: 10000000 INFO @ Thu, 08 Oct 2020 21:19:49: 6000000 INFO @ Thu, 08 Oct 2020 21:19:53: 11000000 INFO @ Thu, 08 Oct 2020 21:19:55: 7000000 INFO @ Thu, 08 Oct 2020 21:20:00: 12000000 INFO @ Thu, 08 Oct 2020 21:20:00: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:20:02: 8000000 INFO @ Thu, 08 Oct 2020 21:20:07: 13000000 INFO @ Thu, 08 Oct 2020 21:20:08: #1 tag size is determined as 64 bps INFO @ Thu, 08 Oct 2020 21:20:08: #1 tag size = 64 INFO @ Thu, 08 Oct 2020 21:20:08: #1 total tags in treatment: 13196376 INFO @ Thu, 08 Oct 2020 21:20:08: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:20:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:20:08: #1 tags after filtering in treatment: 13196376 INFO @ Thu, 08 Oct 2020 21:20:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:20:08: #1 finished! INFO @ Thu, 08 Oct 2020 21:20:08: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:20:09: #2 number of paired peaks: 738 WARNING @ Thu, 08 Oct 2020 21:20:09: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Thu, 08 Oct 2020 21:20:09: start model_add_line... INFO @ Thu, 08 Oct 2020 21:20:09: start X-correlation... INFO @ Thu, 08 Oct 2020 21:20:09: end of X-cor INFO @ Thu, 08 Oct 2020 21:20:09: #2 finished! INFO @ Thu, 08 Oct 2020 21:20:09: #2 predicted fragment length is 54 bps INFO @ Thu, 08 Oct 2020 21:20:09: #2 alternative fragment length(s) may be 2,54 bps INFO @ Thu, 08 Oct 2020 21:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.10_model.r WARNING @ Thu, 08 Oct 2020 21:20:09: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:20:09: #2 You may need to consider one of the other alternative d(s): 2,54 WARNING @ Thu, 08 Oct 2020 21:20:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:20:09: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:20:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:20:09: 9000000 INFO @ Thu, 08 Oct 2020 21:20:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.05_peaks.xls INFO @ Thu, 08 Oct 2020 21:20:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:20:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.05_summits.bed INFO @ Thu, 08 Oct 2020 21:20:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2365 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:20:16: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 21:20:22: 11000000 INFO @ Thu, 08 Oct 2020 21:20:29: 12000000 INFO @ Thu, 08 Oct 2020 21:20:35: 13000000 INFO @ Thu, 08 Oct 2020 21:20:35: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:20:36: #1 tag size is determined as 64 bps INFO @ Thu, 08 Oct 2020 21:20:36: #1 tag size = 64 INFO @ Thu, 08 Oct 2020 21:20:36: #1 total tags in treatment: 13196376 INFO @ Thu, 08 Oct 2020 21:20:36: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:20:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:20:36: #1 tags after filtering in treatment: 13196376 INFO @ Thu, 08 Oct 2020 21:20:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:20:36: #1 finished! INFO @ Thu, 08 Oct 2020 21:20:36: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:20:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:20:37: #2 number of paired peaks: 738 WARNING @ Thu, 08 Oct 2020 21:20:37: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Thu, 08 Oct 2020 21:20:37: start model_add_line... INFO @ Thu, 08 Oct 2020 21:20:37: start X-correlation... INFO @ Thu, 08 Oct 2020 21:20:37: end of X-cor INFO @ Thu, 08 Oct 2020 21:20:37: #2 finished! INFO @ Thu, 08 Oct 2020 21:20:37: #2 predicted fragment length is 54 bps INFO @ Thu, 08 Oct 2020 21:20:37: #2 alternative fragment length(s) may be 2,54 bps INFO @ Thu, 08 Oct 2020 21:20:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.20_model.r WARNING @ Thu, 08 Oct 2020 21:20:37: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:20:37: #2 You may need to consider one of the other alternative d(s): 2,54 WARNING @ Thu, 08 Oct 2020 21:20:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:20:37: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:20:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 21:20:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.10_peaks.xls INFO @ Thu, 08 Oct 2020 21:20:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:20:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.10_summits.bed INFO @ Thu, 08 Oct 2020 21:20:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (987 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:21:03: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:21:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.20_peaks.xls INFO @ Thu, 08 Oct 2020 21:21:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:21:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331156/SRX8331156.20_summits.bed INFO @ Thu, 08 Oct 2020 21:21:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (361 records, 4 fields): 2 millis CompletedMACS2peakCalling