Job ID = 16434978 SRX = SRX11633395 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: 00:04:13 11081177 reads; of these: 11081177 (100.00%) were unpaired; of these: 1029561 (9.29%) aligned 0 times 8539894 (77.07%) aligned exactly 1 time 1511722 (13.64%) aligned >1 times 90.71% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 1226506 / 10051616 = 0.1220 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 10:33:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.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 10:33:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:33:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:34:07: 1000000 INFO @ Tue, 02 Aug 2022 10:34:16: 2000000 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 10:34:25: 3000000 INFO @ Tue, 02 Aug 2022 10:34:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.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 10:34:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:34:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:34:34: 4000000 INFO @ Tue, 02 Aug 2022 10:34:37: 1000000 INFO @ Tue, 02 Aug 2022 10:34:43: 5000000 INFO @ Tue, 02 Aug 2022 10:34:47: 2000000 INFO @ Tue, 02 Aug 2022 10:34:53: 6000000 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 10:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.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 10:34:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:34:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:34:57: 3000000 INFO @ Tue, 02 Aug 2022 10:35:02: 7000000 INFO @ Tue, 02 Aug 2022 10:35:07: 1000000 INFO @ Tue, 02 Aug 2022 10:35:07: 4000000 INFO @ Tue, 02 Aug 2022 10:35:11: 8000000 INFO @ Tue, 02 Aug 2022 10:35:16: 2000000 INFO @ Tue, 02 Aug 2022 10:35:17: 5000000 INFO @ Tue, 02 Aug 2022 10:35:19: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:35:19: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:35:19: #1 total tags in treatment: 8825110 INFO @ Tue, 02 Aug 2022 10:35:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:35:19: #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 10:35:19: #1 tags after filtering in treatment: 8825110 INFO @ Tue, 02 Aug 2022 10:35:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:35:19: #1 finished! INFO @ Tue, 02 Aug 2022 10:35:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:35:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:35:20: #2 number of paired peaks: 271 WARNING @ Tue, 02 Aug 2022 10:35:20: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 02 Aug 2022 10:35:20: start model_add_line... INFO @ Tue, 02 Aug 2022 10:35:20: start X-correlation... INFO @ Tue, 02 Aug 2022 10:35:20: end of X-cor INFO @ Tue, 02 Aug 2022 10:35:20: #2 finished! INFO @ Tue, 02 Aug 2022 10:35:20: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:35:20: #2 alternative fragment length(s) may be 70,569 bps INFO @ Tue, 02 Aug 2022 10:35:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.05_model.r WARNING @ Tue, 02 Aug 2022 10:35:20: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:35:20: #2 You may need to consider one of the other alternative d(s): 70,569 WARNING @ Tue, 02 Aug 2022 10:35:20: #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 10:35:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:35:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:35:25: 3000000 INFO @ Tue, 02 Aug 2022 10:35:28: 6000000 INFO @ Tue, 02 Aug 2022 10:35:34: 4000000 INFO @ Tue, 02 Aug 2022 10:35:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:35:38: 7000000 INFO @ Tue, 02 Aug 2022 10:35:43: 5000000 INFO @ Tue, 02 Aug 2022 10:35:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:35:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:35:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.05_summits.bed INFO @ Tue, 02 Aug 2022 10:35:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:35:48: 8000000 INFO @ Tue, 02 Aug 2022 10:35:53: 6000000 INFO @ Tue, 02 Aug 2022 10:35:56: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:35:56: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:35:56: #1 total tags in treatment: 8825110 INFO @ Tue, 02 Aug 2022 10:35:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:35:56: #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 10:35:56: #1 tags after filtering in treatment: 8825110 INFO @ Tue, 02 Aug 2022 10:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:35:56: #1 finished! INFO @ Tue, 02 Aug 2022 10:35:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:35:57: #2 number of paired peaks: 271 WARNING @ Tue, 02 Aug 2022 10:35:57: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 02 Aug 2022 10:35:57: start model_add_line... INFO @ Tue, 02 Aug 2022 10:35:57: start X-correlation... INFO @ Tue, 02 Aug 2022 10:35:57: end of X-cor INFO @ Tue, 02 Aug 2022 10:35:57: #2 finished! INFO @ Tue, 02 Aug 2022 10:35:57: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:35:57: #2 alternative fragment length(s) may be 70,569 bps INFO @ Tue, 02 Aug 2022 10:35:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.10_model.r WARNING @ Tue, 02 Aug 2022 10:35:57: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:35:57: #2 You may need to consider one of the other alternative d(s): 70,569 WARNING @ Tue, 02 Aug 2022 10:35:57: #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 10:35:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:35:57: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:36:02: 7000000 INFO @ Tue, 02 Aug 2022 10:36:11: 8000000 INFO @ Tue, 02 Aug 2022 10:36:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:36:18: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:36:18: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:36:18: #1 total tags in treatment: 8825110 INFO @ Tue, 02 Aug 2022 10:36:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:36:18: #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 10:36:18: #1 tags after filtering in treatment: 8825110 INFO @ Tue, 02 Aug 2022 10:36:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:36:18: #1 finished! INFO @ Tue, 02 Aug 2022 10:36:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:36:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:36:19: #2 number of paired peaks: 271 WARNING @ Tue, 02 Aug 2022 10:36:19: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 02 Aug 2022 10:36:19: start model_add_line... INFO @ Tue, 02 Aug 2022 10:36:19: start X-correlation... INFO @ Tue, 02 Aug 2022 10:36:19: end of X-cor INFO @ Tue, 02 Aug 2022 10:36:19: #2 finished! INFO @ Tue, 02 Aug 2022 10:36:19: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:36:19: #2 alternative fragment length(s) may be 70,569 bps INFO @ Tue, 02 Aug 2022 10:36:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.20_model.r WARNING @ Tue, 02 Aug 2022 10:36:19: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:36:19: #2 You may need to consider one of the other alternative d(s): 70,569 WARNING @ Tue, 02 Aug 2022 10:36:19: #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 10:36:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:36:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.10_summits.bed INFO @ Tue, 02 Aug 2022 10:36:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (291 records, 4 fields): 34 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:36:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:36:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:36:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:36:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633395/SRX11633395.20_summits.bed INFO @ Tue, 02 Aug 2022 10:36:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 172 millis CompletedMACS2peakCalling