Job ID = 6366999 SRX = SRX257698 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:13:16 prefetch.2.10.7: 1) Downloading 'SRR800715'... 2020-06-15T23:13:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:14:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:14:01 prefetch.2.10.7: 'SRR800715' is valid 2020-06-15T23:14:01 prefetch.2.10.7: 1) 'SRR800715' was downloaded successfully Read 14816963 spots for SRR800715/SRR800715.sra Written 14816963 spots for SRR800715/SRR800715.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: 00:02:22 14816963 reads; of these: 14816963 (100.00%) were unpaired; of these: 39449 (0.27%) aligned 0 times 12302107 (83.03%) aligned exactly 1 time 2475407 (16.71%) aligned >1 times 99.73% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 1634382 / 14777514 = 0.1106 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 08:20:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.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 08:20:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:24: 1000000 INFO @ Tue, 16 Jun 2020 08:20:29: 2000000 INFO @ Tue, 16 Jun 2020 08:20:33: 3000000 INFO @ Tue, 16 Jun 2020 08:20:38: 4000000 INFO @ Tue, 16 Jun 2020 08:20:42: 5000000 INFO @ Tue, 16 Jun 2020 08:20:47: 6000000 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 08:20:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.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 08:20:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:51: 7000000 INFO @ Tue, 16 Jun 2020 08:20:55: 1000000 INFO @ Tue, 16 Jun 2020 08:20:56: 8000000 INFO @ Tue, 16 Jun 2020 08:21:00: 2000000 INFO @ Tue, 16 Jun 2020 08:21:00: 9000000 INFO @ Tue, 16 Jun 2020 08:21:04: 3000000 INFO @ Tue, 16 Jun 2020 08:21:05: 10000000 INFO @ Tue, 16 Jun 2020 08:21:09: 4000000 INFO @ Tue, 16 Jun 2020 08:21:09: 11000000 INFO @ Tue, 16 Jun 2020 08:21:13: 5000000 INFO @ Tue, 16 Jun 2020 08:21:14: 12000000 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 08:21:18: 6000000 INFO @ Tue, 16 Jun 2020 08:21:18: 13000000 INFO @ Tue, 16 Jun 2020 08:21:19: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 08:21:19: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 08:21:19: #1 total tags in treatment: 13143132 INFO @ Tue, 16 Jun 2020 08:21:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:19: #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 08:21:19: #1 tags after filtering in treatment: 13143132 INFO @ Tue, 16 Jun 2020 08:21:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.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 08:21:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:20: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 08:21:20: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:20: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:21:20: #2 alternative fragment length(s) may be 1,22,547 bps INFO @ Tue, 16 Jun 2020 08:21:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.05_model.r WARNING @ Tue, 16 Jun 2020 08:21:20: #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, 16 Jun 2020 08:21:20: #2 You may need to consider one of the other alternative d(s): 1,22,547 WARNING @ Tue, 16 Jun 2020 08:21:20: #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 08:21:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:23: 7000000 INFO @ Tue, 16 Jun 2020 08:21:24: 1000000 INFO @ Tue, 16 Jun 2020 08:21:27: 8000000 INFO @ Tue, 16 Jun 2020 08:21:29: 2000000 INFO @ Tue, 16 Jun 2020 08:21:32: 9000000 INFO @ Tue, 16 Jun 2020 08:21:33: 3000000 INFO @ Tue, 16 Jun 2020 08:21:36: 10000000 INFO @ Tue, 16 Jun 2020 08:21:38: 4000000 INFO @ Tue, 16 Jun 2020 08:21:41: 11000000 INFO @ Tue, 16 Jun 2020 08:21:42: 5000000 INFO @ Tue, 16 Jun 2020 08:21:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:45: 12000000 INFO @ Tue, 16 Jun 2020 08:21:47: 6000000 INFO @ Tue, 16 Jun 2020 08:21:50: 13000000 INFO @ Tue, 16 Jun 2020 08:21:50: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 08:21:50: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 08:21:50: #1 total tags in treatment: 13143132 INFO @ Tue, 16 Jun 2020 08:21:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:50: #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 08:21:50: #1 tags after filtering in treatment: 13143132 INFO @ Tue, 16 Jun 2020 08:21:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:51: 7000000 INFO @ Tue, 16 Jun 2020 08:21:51: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 08:21:51: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:51: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:21:51: #2 alternative fragment length(s) may be 1,22,547 bps INFO @ Tue, 16 Jun 2020 08:21:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.10_model.r WARNING @ Tue, 16 Jun 2020 08:21:51: #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, 16 Jun 2020 08:21:51: #2 You may need to consider one of the other alternative d(s): 1,22,547 WARNING @ Tue, 16 Jun 2020 08:21:51: #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 08:21:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:56: 8000000 INFO @ Tue, 16 Jun 2020 08:22:00: 9000000 INFO @ Tue, 16 Jun 2020 08:22:04: 10000000 INFO @ Tue, 16 Jun 2020 08:22:08: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:13: 12000000 INFO @ Tue, 16 Jun 2020 08:22:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:17: 13000000 INFO @ Tue, 16 Jun 2020 08:22:18: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 08:22:18: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 08:22:18: #1 total tags in treatment: 13143132 INFO @ Tue, 16 Jun 2020 08:22:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:18: #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 08:22:18: #1 tags after filtering in treatment: 13143132 INFO @ Tue, 16 Jun 2020 08:22:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:19: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 08:22:19: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:19: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:22:19: #2 alternative fragment length(s) may be 1,22,547 bps INFO @ Tue, 16 Jun 2020 08:22:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.20_model.r WARNING @ Tue, 16 Jun 2020 08:22:19: #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, 16 Jun 2020 08:22:19: #2 You may need to consider one of the other alternative d(s): 1,22,547 WARNING @ Tue, 16 Jun 2020 08:22:19: #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 08:22:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.10_summits.bed INFO @ Tue, 16 Jun 2020 08:22:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257698/SRX257698.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling