Job ID = 16434902 SRX = SRX10435523 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: 00:05:45 17374353 reads; of these: 17374353 (100.00%) were unpaired; of these: 2067752 (11.90%) aligned 0 times 13012149 (74.89%) aligned exactly 1 time 2294452 (13.21%) aligned >1 times 88.10% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2077758 / 15306601 = 0.1357 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:24:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.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, 02 Aug 2022 10:24:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:24:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:24:31: 1000000 INFO @ Tue, 02 Aug 2022 10:24:38: 2000000 INFO @ Tue, 02 Aug 2022 10:24:45: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:24:51: 4000000 INFO @ Tue, 02 Aug 2022 10:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.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, 02 Aug 2022 10:24:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:24:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:24:58: 5000000 INFO @ Tue, 02 Aug 2022 10:25:01: 1000000 INFO @ Tue, 02 Aug 2022 10:25:05: 6000000 INFO @ Tue, 02 Aug 2022 10:25:09: 2000000 INFO @ Tue, 02 Aug 2022 10:25:11: 7000000 INFO @ Tue, 02 Aug 2022 10:25:16: 3000000 INFO @ Tue, 02 Aug 2022 10:25:18: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:25:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.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, 02 Aug 2022 10:25:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:24: 4000000 INFO @ Tue, 02 Aug 2022 10:25:25: 9000000 INFO @ Tue, 02 Aug 2022 10:25:30: 1000000 INFO @ Tue, 02 Aug 2022 10:25:31: 10000000 INFO @ Tue, 02 Aug 2022 10:25:32: 5000000 INFO @ Tue, 02 Aug 2022 10:25:37: 2000000 INFO @ Tue, 02 Aug 2022 10:25:38: 11000000 INFO @ Tue, 02 Aug 2022 10:25:40: 6000000 INFO @ Tue, 02 Aug 2022 10:25:43: 3000000 INFO @ Tue, 02 Aug 2022 10:25:45: 12000000 INFO @ Tue, 02 Aug 2022 10:25:48: 7000000 INFO @ Tue, 02 Aug 2022 10:25:50: 4000000 INFO @ Tue, 02 Aug 2022 10:25:51: 13000000 INFO @ Tue, 02 Aug 2022 10:25:53: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:25:53: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:25:53: #1 total tags in treatment: 13228843 INFO @ Tue, 02 Aug 2022 10:25:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:25:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:25:53: #1 tags after filtering in treatment: 13228843 INFO @ Tue, 02 Aug 2022 10:25:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:25:53: #1 finished! INFO @ Tue, 02 Aug 2022 10:25:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:25:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:25:54: #2 number of paired peaks: 450 WARNING @ Tue, 02 Aug 2022 10:25:54: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Tue, 02 Aug 2022 10:25:54: start model_add_line... INFO @ Tue, 02 Aug 2022 10:25:54: start X-correlation... INFO @ Tue, 02 Aug 2022 10:25:54: end of X-cor INFO @ Tue, 02 Aug 2022 10:25:54: #2 finished! INFO @ Tue, 02 Aug 2022 10:25:54: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 10:25:54: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 10:25:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.05_model.r WARNING @ Tue, 02 Aug 2022 10:25:54: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:25:54: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Tue, 02 Aug 2022 10:25:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:25:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:25:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:25:56: 8000000 INFO @ Tue, 02 Aug 2022 10:25:56: 5000000 INFO @ Tue, 02 Aug 2022 10:26:02: 6000000 INFO @ Tue, 02 Aug 2022 10:26:04: 9000000 INFO @ Tue, 02 Aug 2022 10:26:09: 7000000 INFO @ Tue, 02 Aug 2022 10:26:11: 10000000 INFO @ Tue, 02 Aug 2022 10:26:15: 8000000 INFO @ Tue, 02 Aug 2022 10:26:19: 11000000 INFO @ Tue, 02 Aug 2022 10:26:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:26:21: 9000000 INFO @ Tue, 02 Aug 2022 10:26:27: 12000000 INFO @ Tue, 02 Aug 2022 10:26:27: 10000000 INFO @ Tue, 02 Aug 2022 10:26:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:26:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:26:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.05_summits.bed INFO @ Tue, 02 Aug 2022 10:26:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2097 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:26:33: 11000000 INFO @ Tue, 02 Aug 2022 10:26:34: 13000000 INFO @ Tue, 02 Aug 2022 10:26:36: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:26:36: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:26:36: #1 total tags in treatment: 13228843 INFO @ Tue, 02 Aug 2022 10:26:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:26:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:26:36: #1 tags after filtering in treatment: 13228843 INFO @ Tue, 02 Aug 2022 10:26:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:26:36: #1 finished! INFO @ Tue, 02 Aug 2022 10:26:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:26:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:26:37: #2 number of paired peaks: 450 WARNING @ Tue, 02 Aug 2022 10:26:37: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Tue, 02 Aug 2022 10:26:37: start model_add_line... INFO @ Tue, 02 Aug 2022 10:26:37: start X-correlation... INFO @ Tue, 02 Aug 2022 10:26:37: end of X-cor INFO @ Tue, 02 Aug 2022 10:26:37: #2 finished! INFO @ Tue, 02 Aug 2022 10:26:37: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 10:26:37: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 10:26:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.10_model.r WARNING @ Tue, 02 Aug 2022 10:26:37: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:26:37: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Tue, 02 Aug 2022 10:26:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:26:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:26:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:26:39: 12000000 INFO @ Tue, 02 Aug 2022 10:26:46: 13000000 INFO @ Tue, 02 Aug 2022 10:26:47: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:26:47: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:26:47: #1 total tags in treatment: 13228843 INFO @ Tue, 02 Aug 2022 10:26:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:26:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:26:47: #1 tags after filtering in treatment: 13228843 INFO @ Tue, 02 Aug 2022 10:26:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:26:47: #1 finished! INFO @ Tue, 02 Aug 2022 10:26:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:26:48: #2 number of paired peaks: 450 WARNING @ Tue, 02 Aug 2022 10:26:48: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Tue, 02 Aug 2022 10:26:48: start model_add_line... INFO @ Tue, 02 Aug 2022 10:26:48: start X-correlation... INFO @ Tue, 02 Aug 2022 10:26:48: end of X-cor INFO @ Tue, 02 Aug 2022 10:26:48: #2 finished! INFO @ Tue, 02 Aug 2022 10:26:48: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 10:26:48: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 10:26:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.20_model.r WARNING @ Tue, 02 Aug 2022 10:26:48: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:26:48: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Tue, 02 Aug 2022 10:26:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:26:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:26:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:27:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:27:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:27:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:27:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.10_summits.bed INFO @ Tue, 02 Aug 2022 10:27:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1377 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:27:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:27:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:27:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435523/SRX10435523.20_summits.bed INFO @ Tue, 02 Aug 2022 10:27:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (838 records, 4 fields): 41 millis CompletedMACS2peakCalling