Job ID = 6368104 SRX = SRX466567 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:58:50 prefetch.2.10.7: 1) Downloading 'SRR1163633'... 2020-06-15T23:58:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:47 prefetch.2.10.7: 1) 'SRR1163633' was downloaded successfully Read 18388946 spots for SRR1163633/SRR1163633.sra Written 18388946 spots for SRR1163633/SRR1163633.sra 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: 00:03:58 18388946 reads; of these: 18388946 (100.00%) were unpaired; of these: 4337259 (23.59%) aligned 0 times 11668019 (63.45%) aligned exactly 1 time 2383668 (12.96%) aligned >1 times 76.41% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 1117787 / 14051687 = 0.0795 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, 16 Jun 2020 09:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.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, 16 Jun 2020 09:09:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:54: 1000000 INFO @ Tue, 16 Jun 2020 09:10:00: 2000000 INFO @ Tue, 16 Jun 2020 09:10:05: 3000000 INFO @ Tue, 16 Jun 2020 09:10:11: 4000000 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, 16 Jun 2020 09:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.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, 16 Jun 2020 09:10:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:18: 5000000 INFO @ Tue, 16 Jun 2020 09:10:25: 6000000 INFO @ Tue, 16 Jun 2020 09:10:25: 1000000 INFO @ Tue, 16 Jun 2020 09:10:31: 7000000 INFO @ Tue, 16 Jun 2020 09:10:32: 2000000 INFO @ Tue, 16 Jun 2020 09:10:37: 8000000 INFO @ Tue, 16 Jun 2020 09:10:38: 3000000 INFO @ Tue, 16 Jun 2020 09:10:43: 9000000 INFO @ Tue, 16 Jun 2020 09:10:45: 4000000 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, 16 Jun 2020 09:10:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.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, 16 Jun 2020 09:10:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:50: 10000000 INFO @ Tue, 16 Jun 2020 09:10:52: 5000000 INFO @ Tue, 16 Jun 2020 09:10:55: 1000000 INFO @ Tue, 16 Jun 2020 09:10:57: 11000000 INFO @ Tue, 16 Jun 2020 09:10:59: 6000000 INFO @ Tue, 16 Jun 2020 09:11:03: 2000000 INFO @ Tue, 16 Jun 2020 09:11:03: 12000000 INFO @ Tue, 16 Jun 2020 09:11:06: 7000000 INFO @ Tue, 16 Jun 2020 09:11:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:10: #1 total tags in treatment: 12933900 INFO @ Tue, 16 Jun 2020 09:11:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:11:10: 3000000 INFO @ Tue, 16 Jun 2020 09:11:10: #1 tags after filtering in treatment: 12933900 INFO @ Tue, 16 Jun 2020 09:11:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:11: #2 number of paired peaks: 325 WARNING @ Tue, 16 Jun 2020 09:11:11: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:11: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:11:11: #2 alternative fragment length(s) may be 2,38 bps INFO @ Tue, 16 Jun 2020 09:11:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:11: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:11: #2 You may need to consider one of the other alternative d(s): 2,38 WARNING @ Tue, 16 Jun 2020 09:11:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:11:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:12: 8000000 INFO @ Tue, 16 Jun 2020 09:11:18: 4000000 INFO @ Tue, 16 Jun 2020 09:11:19: 9000000 INFO @ Tue, 16 Jun 2020 09:11:25: 5000000 INFO @ Tue, 16 Jun 2020 09:11:26: 10000000 INFO @ Tue, 16 Jun 2020 09:11:33: 11000000 INFO @ Tue, 16 Jun 2020 09:11:33: 6000000 INFO @ Tue, 16 Jun 2020 09:11:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:39: 12000000 INFO @ Tue, 16 Jun 2020 09:11:40: 7000000 INFO @ Tue, 16 Jun 2020 09:11:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:46: #1 total tags in treatment: 12933900 INFO @ Tue, 16 Jun 2020 09:11:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:11:46: #1 tags after filtering in treatment: 12933900 INFO @ Tue, 16 Jun 2020 09:11:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:47: #2 number of paired peaks: 325 WARNING @ Tue, 16 Jun 2020 09:11:47: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:47: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:11:47: #2 alternative fragment length(s) may be 2,38 bps INFO @ Tue, 16 Jun 2020 09:11:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.10_model.r WARNING @ Tue, 16 Jun 2020 09:11:47: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:47: #2 You may need to consider one of the other alternative d(s): 2,38 WARNING @ Tue, 16 Jun 2020 09:11:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:11:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:48: 8000000 INFO @ Tue, 16 Jun 2020 09:11:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:55: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:02: 10000000 INFO @ Tue, 16 Jun 2020 09:12:09: 11000000 INFO @ Tue, 16 Jun 2020 09:12:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:17: 12000000 INFO @ Tue, 16 Jun 2020 09:12:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:24: #1 total tags in treatment: 12933900 INFO @ Tue, 16 Jun 2020 09:12:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:12:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:24: Done! INFO @ Tue, 16 Jun 2020 09:12:24: #1 tags after filtering in treatment: 12933900 INFO @ Tue, 16 Jun 2020 09:12:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:24: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:25: #2 number of paired peaks: 325 WARNING @ Tue, 16 Jun 2020 09:12:25: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:25: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:12:25: #2 alternative fragment length(s) may be 2,38 bps INFO @ Tue, 16 Jun 2020 09:12:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.20_model.r WARNING @ Tue, 16 Jun 2020 09:12:25: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:25: #2 You may need to consider one of the other alternative d(s): 2,38 WARNING @ Tue, 16 Jun 2020 09:12:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:12:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466567/SRX466567.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling