Job ID = 6507808 SRX = SRX466520 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:10:06 prefetch.2.10.7: 1) Downloading 'SRR1163586'... 2020-06-26T13:10:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:13:30 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:13:30 prefetch.2.10.7: 1) 'SRR1163586' was downloaded successfully Read 21509609 spots for SRR1163586/SRR1163586.sra Written 21509609 spots for SRR1163586/SRR1163586.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: 00:04:01 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255390 (1.19%) aligned 0 times 17821493 (82.85%) aligned exactly 1 time 3432726 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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] 3668002 / 21254219 = 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 @ Fri, 26 Jun 2020 22:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.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 @ Fri, 26 Jun 2020 22:23:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:23:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:24:04: 1000000 INFO @ Fri, 26 Jun 2020 22:24:09: 2000000 INFO @ Fri, 26 Jun 2020 22:24:14: 3000000 INFO @ Fri, 26 Jun 2020 22:24:20: 4000000 INFO @ Fri, 26 Jun 2020 22:24:25: 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 @ Fri, 26 Jun 2020 22:24:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.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 @ Fri, 26 Jun 2020 22:24:29: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:24:29: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:24:31: 6000000 INFO @ Fri, 26 Jun 2020 22:24:34: 1000000 INFO @ Fri, 26 Jun 2020 22:24:36: 7000000 INFO @ Fri, 26 Jun 2020 22:24:40: 2000000 INFO @ Fri, 26 Jun 2020 22:24:41: 8000000 INFO @ Fri, 26 Jun 2020 22:24:45: 3000000 INFO @ Fri, 26 Jun 2020 22:24:47: 9000000 INFO @ Fri, 26 Jun 2020 22:24:51: 4000000 INFO @ Fri, 26 Jun 2020 22:24:52: 10000000 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 @ Fri, 26 Jun 2020 22:24:57: 5000000 INFO @ Fri, 26 Jun 2020 22:24:57: 11000000 INFO @ Fri, 26 Jun 2020 22:24:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.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 @ Fri, 26 Jun 2020 22:24:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:24:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:25:02: 6000000 INFO @ Fri, 26 Jun 2020 22:25:03: 12000000 INFO @ Fri, 26 Jun 2020 22:25:04: 1000000 INFO @ Fri, 26 Jun 2020 22:25:08: 7000000 INFO @ Fri, 26 Jun 2020 22:25:08: 13000000 INFO @ Fri, 26 Jun 2020 22:25:10: 2000000 INFO @ Fri, 26 Jun 2020 22:25:13: 8000000 INFO @ Fri, 26 Jun 2020 22:25:14: 14000000 INFO @ Fri, 26 Jun 2020 22:25:15: 3000000 INFO @ Fri, 26 Jun 2020 22:25:19: 9000000 INFO @ Fri, 26 Jun 2020 22:25:19: 15000000 INFO @ Fri, 26 Jun 2020 22:25:21: 4000000 INFO @ Fri, 26 Jun 2020 22:25:24: 10000000 INFO @ Fri, 26 Jun 2020 22:25:25: 16000000 INFO @ Fri, 26 Jun 2020 22:25:26: 5000000 INFO @ Fri, 26 Jun 2020 22:25:29: 11000000 INFO @ Fri, 26 Jun 2020 22:25:30: 17000000 INFO @ Fri, 26 Jun 2020 22:25:32: 6000000 INFO @ Fri, 26 Jun 2020 22:25:33: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:25:33: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:25:33: #1 total tags in treatment: 17586217 INFO @ Fri, 26 Jun 2020 22:25:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:25:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:25:33: #1 tags after filtering in treatment: 17586217 INFO @ Fri, 26 Jun 2020 22:25:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:25:33: #1 finished! INFO @ Fri, 26 Jun 2020 22:25:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:25:35: #2 number of paired peaks: 213 WARNING @ Fri, 26 Jun 2020 22:25:35: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Fri, 26 Jun 2020 22:25:35: start model_add_line... INFO @ Fri, 26 Jun 2020 22:25:35: start X-correlation... INFO @ Fri, 26 Jun 2020 22:25:35: end of X-cor INFO @ Fri, 26 Jun 2020 22:25:35: #2 finished! INFO @ Fri, 26 Jun 2020 22:25:35: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:25:35: #2 alternative fragment length(s) may be 1,36,537,543 bps INFO @ Fri, 26 Jun 2020 22:25:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.05_model.r INFO @ Fri, 26 Jun 2020 22:25:35: 12000000 WARNING @ Fri, 26 Jun 2020 22:25:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:25:35: #2 You may need to consider one of the other alternative d(s): 1,36,537,543 WARNING @ Fri, 26 Jun 2020 22:25:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:25:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:25:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:25:37: 7000000 INFO @ Fri, 26 Jun 2020 22:25:40: 13000000 INFO @ Fri, 26 Jun 2020 22:25:43: 8000000 INFO @ Fri, 26 Jun 2020 22:25:46: 14000000 INFO @ Fri, 26 Jun 2020 22:25:48: 9000000 INFO @ Fri, 26 Jun 2020 22:25:51: 15000000 INFO @ Fri, 26 Jun 2020 22:25:53: 10000000 INFO @ Fri, 26 Jun 2020 22:25:57: 16000000 INFO @ Fri, 26 Jun 2020 22:25:58: 11000000 INFO @ Fri, 26 Jun 2020 22:26:02: 17000000 INFO @ Fri, 26 Jun 2020 22:26:03: 12000000 INFO @ Fri, 26 Jun 2020 22:26:05: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:26:05: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:26:05: #1 total tags in treatment: 17586217 INFO @ Fri, 26 Jun 2020 22:26:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:26:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:26:06: #1 tags after filtering in treatment: 17586217 INFO @ Fri, 26 Jun 2020 22:26:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:26:06: #1 finished! INFO @ Fri, 26 Jun 2020 22:26:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:26:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:26:07: #2 number of paired peaks: 213 WARNING @ Fri, 26 Jun 2020 22:26:07: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Fri, 26 Jun 2020 22:26:07: start model_add_line... INFO @ Fri, 26 Jun 2020 22:26:07: start X-correlation... INFO @ Fri, 26 Jun 2020 22:26:07: end of X-cor INFO @ Fri, 26 Jun 2020 22:26:07: #2 finished! INFO @ Fri, 26 Jun 2020 22:26:07: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:26:07: #2 alternative fragment length(s) may be 1,36,537,543 bps INFO @ Fri, 26 Jun 2020 22:26:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.10_model.r WARNING @ Fri, 26 Jun 2020 22:26:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:26:07: #2 You may need to consider one of the other alternative d(s): 1,36,537,543 WARNING @ Fri, 26 Jun 2020 22:26:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:26:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:26:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:26:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:26:08: 13000000 INFO @ Fri, 26 Jun 2020 22:26:14: 14000000 INFO @ Fri, 26 Jun 2020 22:26:19: 15000000 INFO @ Fri, 26 Jun 2020 22:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:26:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.05_summits.bed INFO @ Fri, 26 Jun 2020 22:26:22: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:26:24: 16000000 INFO @ Fri, 26 Jun 2020 22:26:29: 17000000 INFO @ Fri, 26 Jun 2020 22:26:32: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:26:32: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:26:32: #1 total tags in treatment: 17586217 INFO @ Fri, 26 Jun 2020 22:26:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:26:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:26:32: #1 tags after filtering in treatment: 17586217 INFO @ Fri, 26 Jun 2020 22:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:26:32: #1 finished! INFO @ Fri, 26 Jun 2020 22:26:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:26:34: #2 number of paired peaks: 213 WARNING @ Fri, 26 Jun 2020 22:26:34: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Fri, 26 Jun 2020 22:26:34: start model_add_line... INFO @ Fri, 26 Jun 2020 22:26:34: start X-correlation... INFO @ Fri, 26 Jun 2020 22:26:34: end of X-cor INFO @ Fri, 26 Jun 2020 22:26:34: #2 finished! INFO @ Fri, 26 Jun 2020 22:26:34: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:26:34: #2 alternative fragment length(s) may be 1,36,537,543 bps INFO @ Fri, 26 Jun 2020 22:26:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.20_model.r WARNING @ Fri, 26 Jun 2020 22:26:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:26:34: #2 You may need to consider one of the other alternative d(s): 1,36,537,543 WARNING @ Fri, 26 Jun 2020 22:26:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:26:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:26:34: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:26:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:26:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:26:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:26:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.10_summits.bed INFO @ Fri, 26 Jun 2020 22:26:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:27:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:27:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:27:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:27:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466520/SRX466520.20_summits.bed INFO @ Fri, 26 Jun 2020 22:27:21: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling