Job ID = 6529104 SRX = SRX466528 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: 00:04:16 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255415 (1.19%) aligned 0 times 17821487 (82.85%) aligned exactly 1 time 3432707 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 3668239 / 21254194 = 0.1726 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:32:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.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, 30 Jun 2020 01:32:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:32:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:32:47: 1000000 INFO @ Tue, 30 Jun 2020 01:32:52: 2000000 INFO @ Tue, 30 Jun 2020 01:32:57: 3000000 INFO @ Tue, 30 Jun 2020 01:33:02: 4000000 INFO @ Tue, 30 Jun 2020 01:33:07: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:33:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.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, 30 Jun 2020 01:33:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:33:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:33:12: 6000000 INFO @ Tue, 30 Jun 2020 01:33:17: 1000000 INFO @ Tue, 30 Jun 2020 01:33:18: 7000000 INFO @ Tue, 30 Jun 2020 01:33:22: 2000000 INFO @ Tue, 30 Jun 2020 01:33:23: 8000000 INFO @ Tue, 30 Jun 2020 01:33:28: 3000000 INFO @ Tue, 30 Jun 2020 01:33:28: 9000000 INFO @ Tue, 30 Jun 2020 01:33:33: 4000000 INFO @ Tue, 30 Jun 2020 01:33:33: 10000000 INFO @ Tue, 30 Jun 2020 01:33:38: 5000000 INFO @ Tue, 30 Jun 2020 01:33:39: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:33:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.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, 30 Jun 2020 01:33:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:33:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:33:44: 12000000 INFO @ Tue, 30 Jun 2020 01:33:44: 6000000 INFO @ Tue, 30 Jun 2020 01:33:47: 1000000 INFO @ Tue, 30 Jun 2020 01:33:49: 13000000 INFO @ Tue, 30 Jun 2020 01:33:49: 7000000 INFO @ Tue, 30 Jun 2020 01:33:53: 2000000 INFO @ Tue, 30 Jun 2020 01:33:54: 14000000 INFO @ Tue, 30 Jun 2020 01:33:55: 8000000 INFO @ Tue, 30 Jun 2020 01:33:58: 3000000 INFO @ Tue, 30 Jun 2020 01:34:00: 15000000 INFO @ Tue, 30 Jun 2020 01:34:00: 9000000 INFO @ Tue, 30 Jun 2020 01:34:04: 4000000 INFO @ Tue, 30 Jun 2020 01:34:05: 16000000 INFO @ Tue, 30 Jun 2020 01:34:05: 10000000 INFO @ Tue, 30 Jun 2020 01:34:09: 5000000 INFO @ Tue, 30 Jun 2020 01:34:11: 17000000 INFO @ Tue, 30 Jun 2020 01:34:11: 11000000 INFO @ Tue, 30 Jun 2020 01:34:14: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:34:14: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:34:14: #1 total tags in treatment: 17585955 INFO @ Tue, 30 Jun 2020 01:34:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:34:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:34:14: #1 tags after filtering in treatment: 17585955 INFO @ Tue, 30 Jun 2020 01:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:34:14: #1 finished! INFO @ Tue, 30 Jun 2020 01:34:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:34:15: 6000000 INFO @ Tue, 30 Jun 2020 01:34:15: #2 number of paired peaks: 200 WARNING @ Tue, 30 Jun 2020 01:34:15: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 30 Jun 2020 01:34:15: start model_add_line... INFO @ Tue, 30 Jun 2020 01:34:16: start X-correlation... INFO @ Tue, 30 Jun 2020 01:34:16: end of X-cor INFO @ Tue, 30 Jun 2020 01:34:16: #2 finished! INFO @ Tue, 30 Jun 2020 01:34:16: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:34:16: #2 alternative fragment length(s) may be 1,38,585 bps INFO @ Tue, 30 Jun 2020 01:34:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.05_model.r WARNING @ Tue, 30 Jun 2020 01:34:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:34:16: #2 You may need to consider one of the other alternative d(s): 1,38,585 WARNING @ Tue, 30 Jun 2020 01:34:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:34:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:34:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:34:16: 12000000 INFO @ Tue, 30 Jun 2020 01:34:21: 7000000 INFO @ Tue, 30 Jun 2020 01:34:21: 13000000 INFO @ Tue, 30 Jun 2020 01:34:26: 8000000 INFO @ Tue, 30 Jun 2020 01:34:27: 14000000 INFO @ Tue, 30 Jun 2020 01:34:31: 9000000 INFO @ Tue, 30 Jun 2020 01:34:32: 15000000 INFO @ Tue, 30 Jun 2020 01:34:37: 10000000 INFO @ Tue, 30 Jun 2020 01:34:37: 16000000 INFO @ Tue, 30 Jun 2020 01:34:42: 11000000 INFO @ Tue, 30 Jun 2020 01:34:42: 17000000 INFO @ Tue, 30 Jun 2020 01:34:46: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:34:46: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:34:46: #1 total tags in treatment: 17585955 INFO @ Tue, 30 Jun 2020 01:34:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:34:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:34:46: #1 tags after filtering in treatment: 17585955 INFO @ Tue, 30 Jun 2020 01:34:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:34:46: #1 finished! INFO @ Tue, 30 Jun 2020 01:34:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:34:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:34:47: 12000000 INFO @ Tue, 30 Jun 2020 01:34:47: #2 number of paired peaks: 200 WARNING @ Tue, 30 Jun 2020 01:34:47: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 30 Jun 2020 01:34:47: start model_add_line... INFO @ Tue, 30 Jun 2020 01:34:47: start X-correlation... INFO @ Tue, 30 Jun 2020 01:34:47: end of X-cor INFO @ Tue, 30 Jun 2020 01:34:47: #2 finished! INFO @ Tue, 30 Jun 2020 01:34:47: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:34:47: #2 alternative fragment length(s) may be 1,38,585 bps INFO @ Tue, 30 Jun 2020 01:34:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.10_model.r WARNING @ Tue, 30 Jun 2020 01:34:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:34:47: #2 You may need to consider one of the other alternative d(s): 1,38,585 WARNING @ Tue, 30 Jun 2020 01:34:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:34:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:34:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:34:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:34:52: 13000000 INFO @ Tue, 30 Jun 2020 01:34:57: 14000000 INFO @ Tue, 30 Jun 2020 01:35:03: 15000000 INFO @ Tue, 30 Jun 2020 01:35:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:35:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.05_summits.bed INFO @ Tue, 30 Jun 2020 01:35:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:35:08: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:35:13: 17000000 INFO @ Tue, 30 Jun 2020 01:35:16: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:35:16: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:35:16: #1 total tags in treatment: 17585955 INFO @ Tue, 30 Jun 2020 01:35:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:35:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:35:17: #1 tags after filtering in treatment: 17585955 INFO @ Tue, 30 Jun 2020 01:35:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:35:17: #1 finished! INFO @ Tue, 30 Jun 2020 01:35:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:35:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:35:18: #2 number of paired peaks: 200 WARNING @ Tue, 30 Jun 2020 01:35:18: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 30 Jun 2020 01:35:18: start model_add_line... INFO @ Tue, 30 Jun 2020 01:35:18: start X-correlation... INFO @ Tue, 30 Jun 2020 01:35:18: end of X-cor INFO @ Tue, 30 Jun 2020 01:35:18: #2 finished! INFO @ Tue, 30 Jun 2020 01:35:18: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:35:18: #2 alternative fragment length(s) may be 1,38,585 bps INFO @ Tue, 30 Jun 2020 01:35:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.20_model.r WARNING @ Tue, 30 Jun 2020 01:35:18: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:35:18: #2 You may need to consider one of the other alternative d(s): 1,38,585 WARNING @ Tue, 30 Jun 2020 01:35:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:35:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:35:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:35:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:35:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:35:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:35:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.10_summits.bed INFO @ Tue, 30 Jun 2020 01:35:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:35:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:36:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:36:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:36:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466528/SRX466528.20_summits.bed INFO @ Tue, 30 Jun 2020 01:36:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling