Job ID = 14160749 SRX = SRX10399031 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: 00:04:17 13764712 reads; of these: 13764712 (100.00%) were unpaired; of these: 501159 (3.64%) aligned 0 times 11092147 (80.58%) aligned exactly 1 time 2171406 (15.78%) aligned >1 times 96.36% overall alignment rate Time searching: 00:04:17 Overall time: 00:04:17 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] 1219748 / 13263553 = 0.0920 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 04:10:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.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 04:10:41: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:10:41: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:10:47: 1000000 INFO @ Thu, 09 Dec 2021 04:10:54: 2000000 INFO @ Thu, 09 Dec 2021 04:11:00: 3000000 INFO @ Thu, 09 Dec 2021 04:11:06: 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 04:11:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.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 04:11:11: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:11:11: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:11:13: 5000000 INFO @ Thu, 09 Dec 2021 04:11:17: 1000000 INFO @ Thu, 09 Dec 2021 04:11:20: 6000000 INFO @ Thu, 09 Dec 2021 04:11:23: 2000000 INFO @ Thu, 09 Dec 2021 04:11:26: 7000000 INFO @ Thu, 09 Dec 2021 04:11:29: 3000000 INFO @ Thu, 09 Dec 2021 04:11:33: 8000000 INFO @ Thu, 09 Dec 2021 04:11:35: 4000000 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 04:11:40: 9000000 INFO @ Thu, 09 Dec 2021 04:11:41: 5000000 INFO @ Thu, 09 Dec 2021 04:11:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.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 04:11:41: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:11:41: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:11:47: 10000000 INFO @ Thu, 09 Dec 2021 04:11:47: 6000000 INFO @ Thu, 09 Dec 2021 04:11:48: 1000000 INFO @ Thu, 09 Dec 2021 04:11:53: 7000000 INFO @ Thu, 09 Dec 2021 04:11:54: 11000000 INFO @ Thu, 09 Dec 2021 04:11:55: 2000000 INFO @ Thu, 09 Dec 2021 04:11:59: 8000000 INFO @ Thu, 09 Dec 2021 04:12:00: 12000000 INFO @ Thu, 09 Dec 2021 04:12:01: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:12:01: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:12:01: #1 total tags in treatment: 12043805 INFO @ Thu, 09 Dec 2021 04:12:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:12:01: #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 04:12:01: #1 tags after filtering in treatment: 12043805 INFO @ Thu, 09 Dec 2021 04:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:12:01: #1 finished! INFO @ Thu, 09 Dec 2021 04:12:01: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:12:02: 3000000 INFO @ Thu, 09 Dec 2021 04:12:02: #2 number of paired peaks: 267 WARNING @ Thu, 09 Dec 2021 04:12:02: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Thu, 09 Dec 2021 04:12:02: start model_add_line... INFO @ Thu, 09 Dec 2021 04:12:02: start X-correlation... INFO @ Thu, 09 Dec 2021 04:12:02: end of X-cor INFO @ Thu, 09 Dec 2021 04:12:02: #2 finished! INFO @ Thu, 09 Dec 2021 04:12:02: #2 predicted fragment length is 75 bps INFO @ Thu, 09 Dec 2021 04:12:02: #2 alternative fragment length(s) may be 4,75 bps INFO @ Thu, 09 Dec 2021 04:12:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.05_model.r WARNING @ Thu, 09 Dec 2021 04:12:02: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:12:02: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Thu, 09 Dec 2021 04:12:02: #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 04:12:02: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:12:05: 9000000 INFO @ Thu, 09 Dec 2021 04:12:08: 4000000 INFO @ Thu, 09 Dec 2021 04:12:11: 10000000 INFO @ Thu, 09 Dec 2021 04:12:15: 5000000 INFO @ Thu, 09 Dec 2021 04:12:17: 11000000 INFO @ Thu, 09 Dec 2021 04:12:22: 6000000 INFO @ Thu, 09 Dec 2021 04:12:23: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:12:23: 12000000 INFO @ Thu, 09 Dec 2021 04:12:23: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:12:23: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:12:23: #1 total tags in treatment: 12043805 INFO @ Thu, 09 Dec 2021 04:12:23: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:12:23: #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 04:12:24: #1 tags after filtering in treatment: 12043805 INFO @ Thu, 09 Dec 2021 04:12:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:12:24: #1 finished! INFO @ Thu, 09 Dec 2021 04:12:24: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:12:24: #2 number of paired peaks: 267 WARNING @ Thu, 09 Dec 2021 04:12:24: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Thu, 09 Dec 2021 04:12:24: start model_add_line... INFO @ Thu, 09 Dec 2021 04:12:25: start X-correlation... INFO @ Thu, 09 Dec 2021 04:12:25: end of X-cor INFO @ Thu, 09 Dec 2021 04:12:25: #2 finished! INFO @ Thu, 09 Dec 2021 04:12:25: #2 predicted fragment length is 75 bps INFO @ Thu, 09 Dec 2021 04:12:25: #2 alternative fragment length(s) may be 4,75 bps INFO @ Thu, 09 Dec 2021 04:12:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.10_model.r WARNING @ Thu, 09 Dec 2021 04:12:25: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:12:25: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Thu, 09 Dec 2021 04:12:25: #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 04:12:25: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:12:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:12:28: 7000000 INFO @ Thu, 09 Dec 2021 04:12:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:12:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:12:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.05_summits.bed INFO @ Thu, 09 Dec 2021 04:12:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (577 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:12:35: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:12:41: 9000000 INFO @ Thu, 09 Dec 2021 04:12:47: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:12:48: 10000000 INFO @ Thu, 09 Dec 2021 04:12:54: 11000000 INFO @ Thu, 09 Dec 2021 04:12:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:12:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:12:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.10_summits.bed INFO @ Thu, 09 Dec 2021 04:12:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:13:00: 12000000 INFO @ Thu, 09 Dec 2021 04:13:01: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:13:01: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:13:01: #1 total tags in treatment: 12043805 INFO @ Thu, 09 Dec 2021 04:13:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:13:01: #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 04:13:01: #1 tags after filtering in treatment: 12043805 INFO @ Thu, 09 Dec 2021 04:13:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:13:01: #1 finished! INFO @ Thu, 09 Dec 2021 04:13:01: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:13:02: #2 number of paired peaks: 267 WARNING @ Thu, 09 Dec 2021 04:13:02: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Thu, 09 Dec 2021 04:13:02: start model_add_line... INFO @ Thu, 09 Dec 2021 04:13:02: start X-correlation... INFO @ Thu, 09 Dec 2021 04:13:02: end of X-cor INFO @ Thu, 09 Dec 2021 04:13:02: #2 finished! INFO @ Thu, 09 Dec 2021 04:13:02: #2 predicted fragment length is 75 bps INFO @ Thu, 09 Dec 2021 04:13:02: #2 alternative fragment length(s) may be 4,75 bps INFO @ Thu, 09 Dec 2021 04:13:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.20_model.r WARNING @ Thu, 09 Dec 2021 04:13:02: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:13:02: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Thu, 09 Dec 2021 04:13:02: #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 04:13:02: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:13:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:13:24: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399031/SRX10399031.20_summits.bed INFO @ Thu, 09 Dec 2021 04:13:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 1 millis CompletedMACS2peakCalling