Job ID = 14160710 SRX = SRX10399029 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: 00:03:51 12305094 reads; of these: 12305094 (100.00%) were unpaired; of these: 3356681 (27.28%) aligned 0 times 7437455 (60.44%) aligned exactly 1 time 1510958 (12.28%) aligned >1 times 72.72% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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] 794910 / 8948413 = 0.0888 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:56:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.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, 09 Dec 2021 03:56:01: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:56:01: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:56:08: 1000000 INFO @ Thu, 09 Dec 2021 03:56:14: 2000000 INFO @ Thu, 09 Dec 2021 03:56:21: 3000000 INFO @ Thu, 09 Dec 2021 03:56:28: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:56:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.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, 09 Dec 2021 03:56:31: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:56:31: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:56:35: 5000000 INFO @ Thu, 09 Dec 2021 03:56:37: 1000000 INFO @ Thu, 09 Dec 2021 03:56:42: 6000000 INFO @ Thu, 09 Dec 2021 03:56:43: 2000000 INFO @ Thu, 09 Dec 2021 03:56:49: 7000000 INFO @ Thu, 09 Dec 2021 03:56:50: 3000000 INFO @ Thu, 09 Dec 2021 03:56:56: 8000000 INFO @ Thu, 09 Dec 2021 03:56:56: 4000000 INFO @ Thu, 09 Dec 2021 03:56:57: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:56:57: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:56:57: #1 total tags in treatment: 8153503 INFO @ Thu, 09 Dec 2021 03:56:57: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:56:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:56:57: #1 tags after filtering in treatment: 8153503 INFO @ Thu, 09 Dec 2021 03:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:56:57: #1 finished! INFO @ Thu, 09 Dec 2021 03:56:57: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:56:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:56:57: #2 number of paired peaks: 392 WARNING @ Thu, 09 Dec 2021 03:56:57: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Thu, 09 Dec 2021 03:56:57: start model_add_line... INFO @ Thu, 09 Dec 2021 03:56:57: start X-correlation... INFO @ Thu, 09 Dec 2021 03:56:57: end of X-cor INFO @ Thu, 09 Dec 2021 03:56:57: #2 finished! INFO @ Thu, 09 Dec 2021 03:56:57: #2 predicted fragment length is 89 bps INFO @ Thu, 09 Dec 2021 03:56:57: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 09 Dec 2021 03:56:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.05_model.r WARNING @ Thu, 09 Dec 2021 03:56:57: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:56:57: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Thu, 09 Dec 2021 03:56:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:56:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:56:57: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.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, 09 Dec 2021 03:57:01: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:57:01: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:57:02: 5000000 INFO @ Thu, 09 Dec 2021 03:57:07: 1000000 INFO @ Thu, 09 Dec 2021 03:57:08: 6000000 INFO @ Thu, 09 Dec 2021 03:57:13: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:57:13: 2000000 INFO @ Thu, 09 Dec 2021 03:57:14: 7000000 INFO @ Thu, 09 Dec 2021 03:57:19: 3000000 INFO @ Thu, 09 Dec 2021 03:57:20: 8000000 INFO @ Thu, 09 Dec 2021 03:57:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:57:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:57:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.05_summits.bed INFO @ Thu, 09 Dec 2021 03:57:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1043 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:57:21: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:57:21: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:57:21: #1 total tags in treatment: 8153503 INFO @ Thu, 09 Dec 2021 03:57:21: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:57:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:57:21: #1 tags after filtering in treatment: 8153503 INFO @ Thu, 09 Dec 2021 03:57:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:57:21: #1 finished! INFO @ Thu, 09 Dec 2021 03:57:21: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:57:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:57:22: #2 number of paired peaks: 392 WARNING @ Thu, 09 Dec 2021 03:57:22: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Thu, 09 Dec 2021 03:57:22: start model_add_line... INFO @ Thu, 09 Dec 2021 03:57:22: start X-correlation... INFO @ Thu, 09 Dec 2021 03:57:22: end of X-cor INFO @ Thu, 09 Dec 2021 03:57:22: #2 finished! INFO @ Thu, 09 Dec 2021 03:57:22: #2 predicted fragment length is 89 bps INFO @ Thu, 09 Dec 2021 03:57:22: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 09 Dec 2021 03:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.10_model.r WARNING @ Thu, 09 Dec 2021 03:57:22: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:57:22: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Thu, 09 Dec 2021 03:57:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:57:22: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:57:25: 4000000 INFO @ Thu, 09 Dec 2021 03:57:31: 5000000 INFO @ Thu, 09 Dec 2021 03:57:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:57:37: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:57:43: 7000000 INFO @ Thu, 09 Dec 2021 03:57:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:57:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:57:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.10_summits.bed INFO @ Thu, 09 Dec 2021 03:57:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (641 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:57:49: 8000000 INFO @ Thu, 09 Dec 2021 03:57:49: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:57:49: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:57:49: #1 total tags in treatment: 8153503 INFO @ Thu, 09 Dec 2021 03:57:49: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:57:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:57:50: #1 tags after filtering in treatment: 8153503 INFO @ Thu, 09 Dec 2021 03:57:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:57:50: #1 finished! INFO @ Thu, 09 Dec 2021 03:57:50: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:57:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:57:50: #2 number of paired peaks: 392 WARNING @ Thu, 09 Dec 2021 03:57:50: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Thu, 09 Dec 2021 03:57:50: start model_add_line... INFO @ Thu, 09 Dec 2021 03:57:50: start X-correlation... INFO @ Thu, 09 Dec 2021 03:57:50: end of X-cor INFO @ Thu, 09 Dec 2021 03:57:50: #2 finished! INFO @ Thu, 09 Dec 2021 03:57:50: #2 predicted fragment length is 89 bps INFO @ Thu, 09 Dec 2021 03:57:50: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 09 Dec 2021 03:57:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.20_model.r WARNING @ Thu, 09 Dec 2021 03:57:50: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:57:50: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Thu, 09 Dec 2021 03:57:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:57:50: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:57:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:58:05: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:58:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:58:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:58:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399029/SRX10399029.20_summits.bed INFO @ Thu, 09 Dec 2021 03:58:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 1 millis CompletedMACS2peakCalling