Job ID = 6368018 SRX = SRX466481 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:08:54 prefetch.2.10.7: 1) Downloading 'SRR1163547'... 2020-06-16T00:08:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:12:29 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:12:29 prefetch.2.10.7: 1) 'SRR1163547' was downloaded successfully Read 19609564 spots for SRR1163547/SRR1163547.sra Written 19609564 spots for SRR1163547/SRR1163547.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: 00:04:52 19609564 reads; of these: 19609564 (100.00%) were unpaired; of these: 899048 (4.58%) aligned 0 times 14523463 (74.06%) aligned exactly 1 time 4187053 (21.35%) aligned >1 times 95.42% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 5402278 / 18710516 = 0.2887 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 09:23:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.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 09:23:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:20: 1000000 INFO @ Tue, 16 Jun 2020 09:23:26: 2000000 INFO @ Tue, 16 Jun 2020 09:23:32: 3000000 INFO @ Tue, 16 Jun 2020 09:23:38: 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 09:23:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.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 09:23:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:44: 5000000 INFO @ Tue, 16 Jun 2020 09:23:50: 1000000 INFO @ Tue, 16 Jun 2020 09:23:51: 6000000 INFO @ Tue, 16 Jun 2020 09:23:57: 2000000 INFO @ Tue, 16 Jun 2020 09:23:58: 7000000 INFO @ Tue, 16 Jun 2020 09:24:03: 3000000 INFO @ Tue, 16 Jun 2020 09:24:05: 8000000 INFO @ Tue, 16 Jun 2020 09:24:10: 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 09:24:12: 9000000 INFO @ Tue, 16 Jun 2020 09:24:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.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 09:24:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:17: 5000000 INFO @ Tue, 16 Jun 2020 09:24:19: 10000000 INFO @ Tue, 16 Jun 2020 09:24:20: 1000000 INFO @ Tue, 16 Jun 2020 09:24:23: 6000000 INFO @ Tue, 16 Jun 2020 09:24:26: 11000000 INFO @ Tue, 16 Jun 2020 09:24:27: 2000000 INFO @ Tue, 16 Jun 2020 09:24:30: 7000000 INFO @ Tue, 16 Jun 2020 09:24:32: 12000000 INFO @ Tue, 16 Jun 2020 09:24:34: 3000000 INFO @ Tue, 16 Jun 2020 09:24:37: 8000000 INFO @ Tue, 16 Jun 2020 09:24:39: 13000000 INFO @ Tue, 16 Jun 2020 09:24:40: 4000000 INFO @ Tue, 16 Jun 2020 09:24:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:24:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:24:41: #1 total tags in treatment: 13308238 INFO @ Tue, 16 Jun 2020 09:24:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:41: #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 09:24:42: #1 tags after filtering in treatment: 13308238 INFO @ Tue, 16 Jun 2020 09:24:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:42: #2 number of paired peaks: 478 WARNING @ Tue, 16 Jun 2020 09:24:42: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:43: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:24:43: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 09:24:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.05_model.r WARNING @ Tue, 16 Jun 2020 09:24:43: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:24:43: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 09:24:43: #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 09:24:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:24:43: 9000000 INFO @ Tue, 16 Jun 2020 09:24:47: 5000000 INFO @ Tue, 16 Jun 2020 09:24:50: 10000000 INFO @ Tue, 16 Jun 2020 09:24:54: 6000000 INFO @ Tue, 16 Jun 2020 09:24:57: 11000000 INFO @ Tue, 16 Jun 2020 09:25:01: 7000000 INFO @ Tue, 16 Jun 2020 09:25:04: 12000000 INFO @ Tue, 16 Jun 2020 09:25:08: 8000000 INFO @ Tue, 16 Jun 2020 09:25:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:10: 13000000 INFO @ Tue, 16 Jun 2020 09:25:12: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:25:12: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:25:12: #1 total tags in treatment: 13308238 INFO @ Tue, 16 Jun 2020 09:25:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:12: #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 09:25:13: #1 tags after filtering in treatment: 13308238 INFO @ Tue, 16 Jun 2020 09:25:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:14: #2 number of paired peaks: 478 WARNING @ Tue, 16 Jun 2020 09:25:14: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:14: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:25:14: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 09:25:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.10_model.r WARNING @ Tue, 16 Jun 2020 09:25:14: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:14: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 09:25:14: #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 09:25:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:15: 9000000 INFO @ Tue, 16 Jun 2020 09:25:21: 10000000 INFO @ Tue, 16 Jun 2020 09:25:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.05_summits.bed INFO @ Tue, 16 Jun 2020 09:25:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (831 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:25:27: 11000000 INFO @ Tue, 16 Jun 2020 09:25:34: 12000000 INFO @ Tue, 16 Jun 2020 09:25:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:40: 13000000 INFO @ Tue, 16 Jun 2020 09:25:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:25:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:25:42: #1 total tags in treatment: 13308238 INFO @ Tue, 16 Jun 2020 09:25:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:42: #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 09:25:42: #1 tags after filtering in treatment: 13308238 INFO @ Tue, 16 Jun 2020 09:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:43: #2 number of paired peaks: 478 WARNING @ Tue, 16 Jun 2020 09:25:43: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:43: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:25:43: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 09:25:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.20_model.r WARNING @ Tue, 16 Jun 2020 09:25:43: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:43: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 09:25:43: #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 09:25:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.10_summits.bed INFO @ Tue, 16 Jun 2020 09:25:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (518 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:26:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466481/SRX466481.20_summits.bed INFO @ Tue, 16 Jun 2020 09:26:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (201 records, 4 fields): 2 millis CompletedMACS2peakCalling