Job ID = 14158085 SRX = SRX10040019 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: 00:05:46 20334401 reads; of these: 20334401 (100.00%) were unpaired; of these: 478641 (2.35%) aligned 0 times 15998209 (78.68%) aligned exactly 1 time 3857551 (18.97%) aligned >1 times 97.65% 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 12 files... [bam_rmdupse_core] 3601700 / 19855760 = 0.1814 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 @ Wed, 08 Dec 2021 14:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.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 @ Wed, 08 Dec 2021 14:29:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:29:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:29:41: 1000000 INFO @ Wed, 08 Dec 2021 14:29:47: 2000000 INFO @ Wed, 08 Dec 2021 14:29:53: 3000000 INFO @ Wed, 08 Dec 2021 14:29:59: 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 @ Wed, 08 Dec 2021 14:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.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 @ Wed, 08 Dec 2021 14:30:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:30:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:30:05: 5000000 INFO @ Wed, 08 Dec 2021 14:30:11: 1000000 INFO @ Wed, 08 Dec 2021 14:30:12: 6000000 INFO @ Wed, 08 Dec 2021 14:30:18: 2000000 INFO @ Wed, 08 Dec 2021 14:30:19: 7000000 INFO @ Wed, 08 Dec 2021 14:30:25: 3000000 INFO @ Wed, 08 Dec 2021 14:30:25: 8000000 INFO @ Wed, 08 Dec 2021 14:30:32: 4000000 INFO @ Wed, 08 Dec 2021 14:30:32: 9000000 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 @ Wed, 08 Dec 2021 14:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.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 @ Wed, 08 Dec 2021 14:30:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:30:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:30:38: 5000000 INFO @ Wed, 08 Dec 2021 14:30:39: 10000000 INFO @ Wed, 08 Dec 2021 14:30:42: 1000000 INFO @ Wed, 08 Dec 2021 14:30:45: 6000000 INFO @ Wed, 08 Dec 2021 14:30:46: 11000000 INFO @ Wed, 08 Dec 2021 14:30:48: 2000000 INFO @ Wed, 08 Dec 2021 14:30:52: 7000000 INFO @ Wed, 08 Dec 2021 14:30:52: 12000000 INFO @ Wed, 08 Dec 2021 14:30:55: 3000000 INFO @ Wed, 08 Dec 2021 14:30:59: 8000000 INFO @ Wed, 08 Dec 2021 14:30:59: 13000000 INFO @ Wed, 08 Dec 2021 14:31:02: 4000000 INFO @ Wed, 08 Dec 2021 14:31:06: 9000000 INFO @ Wed, 08 Dec 2021 14:31:06: 14000000 INFO @ Wed, 08 Dec 2021 14:31:09: 5000000 INFO @ Wed, 08 Dec 2021 14:31:13: 10000000 INFO @ Wed, 08 Dec 2021 14:31:13: 15000000 INFO @ Wed, 08 Dec 2021 14:31:16: 6000000 INFO @ Wed, 08 Dec 2021 14:31:19: 11000000 INFO @ Wed, 08 Dec 2021 14:31:19: 16000000 INFO @ Wed, 08 Dec 2021 14:31:21: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:31:21: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:31:21: #1 total tags in treatment: 16254060 INFO @ Wed, 08 Dec 2021 14:31:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:31:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:31:21: #1 tags after filtering in treatment: 16254060 INFO @ Wed, 08 Dec 2021 14:31:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:31:21: #1 finished! INFO @ Wed, 08 Dec 2021 14:31:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:31:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:31:22: #2 number of paired peaks: 164 WARNING @ Wed, 08 Dec 2021 14:31:22: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Wed, 08 Dec 2021 14:31:22: start model_add_line... INFO @ Wed, 08 Dec 2021 14:31:22: start X-correlation... INFO @ Wed, 08 Dec 2021 14:31:22: end of X-cor INFO @ Wed, 08 Dec 2021 14:31:22: #2 finished! INFO @ Wed, 08 Dec 2021 14:31:22: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:31:22: #2 alternative fragment length(s) may be 1,51,452,511,567,582,594,596 bps INFO @ Wed, 08 Dec 2021 14:31:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.05_model.r WARNING @ Wed, 08 Dec 2021 14:31:23: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:31:23: #2 You may need to consider one of the other alternative d(s): 1,51,452,511,567,582,594,596 WARNING @ Wed, 08 Dec 2021 14:31:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:31:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:31:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:31:23: 7000000 INFO @ Wed, 08 Dec 2021 14:31:26: 12000000 INFO @ Wed, 08 Dec 2021 14:31:30: 8000000 INFO @ Wed, 08 Dec 2021 14:31:33: 13000000 INFO @ Wed, 08 Dec 2021 14:31:36: 9000000 INFO @ Wed, 08 Dec 2021 14:31:39: 14000000 INFO @ Wed, 08 Dec 2021 14:31:43: 10000000 INFO @ Wed, 08 Dec 2021 14:31:46: 15000000 INFO @ Wed, 08 Dec 2021 14:31:48: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:31:50: 11000000 INFO @ Wed, 08 Dec 2021 14:31:53: 16000000 INFO @ Wed, 08 Dec 2021 14:31:54: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:31:54: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:31:54: #1 total tags in treatment: 16254060 INFO @ Wed, 08 Dec 2021 14:31:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:31:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:31:55: #1 tags after filtering in treatment: 16254060 INFO @ Wed, 08 Dec 2021 14:31:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:31:55: #1 finished! INFO @ Wed, 08 Dec 2021 14:31:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:31:56: #2 number of paired peaks: 164 WARNING @ Wed, 08 Dec 2021 14:31:56: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Wed, 08 Dec 2021 14:31:56: start model_add_line... INFO @ Wed, 08 Dec 2021 14:31:56: start X-correlation... INFO @ Wed, 08 Dec 2021 14:31:56: end of X-cor INFO @ Wed, 08 Dec 2021 14:31:56: #2 finished! INFO @ Wed, 08 Dec 2021 14:31:56: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:31:56: #2 alternative fragment length(s) may be 1,51,452,511,567,582,594,596 bps INFO @ Wed, 08 Dec 2021 14:31:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.10_model.r WARNING @ Wed, 08 Dec 2021 14:31:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:31:56: #2 You may need to consider one of the other alternative d(s): 1,51,452,511,567,582,594,596 WARNING @ Wed, 08 Dec 2021 14:31:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:31:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:31:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:31:56: 12000000 INFO @ Wed, 08 Dec 2021 14:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.05_summits.bed INFO @ Wed, 08 Dec 2021 14:32:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:32:02: 13000000 INFO @ Wed, 08 Dec 2021 14:32:08: 14000000 INFO @ Wed, 08 Dec 2021 14:32:14: 15000000 INFO @ Wed, 08 Dec 2021 14:32:20: 16000000 INFO @ Wed, 08 Dec 2021 14:32:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:32:22: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:32:22: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:32:22: #1 total tags in treatment: 16254060 INFO @ Wed, 08 Dec 2021 14:32:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:32:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:32:22: #1 tags after filtering in treatment: 16254060 INFO @ Wed, 08 Dec 2021 14:32:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:32:22: #1 finished! INFO @ Wed, 08 Dec 2021 14:32:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:32:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:32:23: #2 number of paired peaks: 164 WARNING @ Wed, 08 Dec 2021 14:32:23: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Wed, 08 Dec 2021 14:32:23: start model_add_line... INFO @ Wed, 08 Dec 2021 14:32:23: start X-correlation... INFO @ Wed, 08 Dec 2021 14:32:23: end of X-cor INFO @ Wed, 08 Dec 2021 14:32:23: #2 finished! INFO @ Wed, 08 Dec 2021 14:32:23: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:32:23: #2 alternative fragment length(s) may be 1,51,452,511,567,582,594,596 bps INFO @ Wed, 08 Dec 2021 14:32:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.20_model.r WARNING @ Wed, 08 Dec 2021 14:32:23: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:32:23: #2 You may need to consider one of the other alternative d(s): 1,51,452,511,567,582,594,596 WARNING @ Wed, 08 Dec 2021 14:32:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:32:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:32:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:32:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:32:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:32:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.10_summits.bed INFO @ Wed, 08 Dec 2021 14:32:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:32:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:33:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:33:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:33:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040019/SRX10040019.20_summits.bed INFO @ Wed, 08 Dec 2021 14:33:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling