Job ID = 6507825 SRX = SRX494829 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:48:42 prefetch.2.10.7: 1) Downloading 'SRR1198361'... 2020-06-26T13:48:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:50:56 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:50:56 prefetch.2.10.7: 1) 'SRR1198361' was downloaded successfully Read 29041160 spots for SRR1198361/SRR1198361.sra Written 29041160 spots for SRR1198361/SRR1198361.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: 00:04:24 29041160 reads; of these: 29041160 (100.00%) were unpaired; of these: 10749460 (37.01%) aligned 0 times 15214186 (52.39%) aligned exactly 1 time 3077514 (10.60%) aligned >1 times 62.99% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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] 1906660 / 18291700 = 0.1042 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 23:01:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.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 23:01:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:01:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:01:26: 1000000 INFO @ Fri, 26 Jun 2020 23:01:31: 2000000 INFO @ Fri, 26 Jun 2020 23:01:37: 3000000 INFO @ Fri, 26 Jun 2020 23:01:43: 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 @ Fri, 26 Jun 2020 23:01:49: 5000000 INFO @ Fri, 26 Jun 2020 23:01:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.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 23:01:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:01:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:01:56: 6000000 INFO @ Fri, 26 Jun 2020 23:01:56: 1000000 INFO @ Fri, 26 Jun 2020 23:02:02: 7000000 INFO @ Fri, 26 Jun 2020 23:02:03: 2000000 INFO @ Fri, 26 Jun 2020 23:02:09: 8000000 INFO @ Fri, 26 Jun 2020 23:02:09: 3000000 INFO @ Fri, 26 Jun 2020 23:02:15: 9000000 INFO @ Fri, 26 Jun 2020 23:02:15: 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 @ Fri, 26 Jun 2020 23:02:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.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 23:02:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:02:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:02:22: 10000000 INFO @ Fri, 26 Jun 2020 23:02:22: 5000000 INFO @ Fri, 26 Jun 2020 23:02:27: 1000000 INFO @ Fri, 26 Jun 2020 23:02:29: 11000000 INFO @ Fri, 26 Jun 2020 23:02:29: 6000000 INFO @ Fri, 26 Jun 2020 23:02:35: 2000000 INFO @ Fri, 26 Jun 2020 23:02:36: 7000000 INFO @ Fri, 26 Jun 2020 23:02:37: 12000000 INFO @ Fri, 26 Jun 2020 23:02:42: 3000000 INFO @ Fri, 26 Jun 2020 23:02:43: 8000000 INFO @ Fri, 26 Jun 2020 23:02:44: 13000000 INFO @ Fri, 26 Jun 2020 23:02:49: 4000000 INFO @ Fri, 26 Jun 2020 23:02:50: 9000000 INFO @ Fri, 26 Jun 2020 23:02:51: 14000000 INFO @ Fri, 26 Jun 2020 23:02:56: 5000000 INFO @ Fri, 26 Jun 2020 23:02:57: 10000000 INFO @ Fri, 26 Jun 2020 23:02:58: 15000000 INFO @ Fri, 26 Jun 2020 23:03:03: 6000000 INFO @ Fri, 26 Jun 2020 23:03:05: 11000000 INFO @ Fri, 26 Jun 2020 23:03:05: 16000000 INFO @ Fri, 26 Jun 2020 23:03:08: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:03:08: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:03:08: #1 total tags in treatment: 16385040 INFO @ Fri, 26 Jun 2020 23:03:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:03:08: #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 23:03:08: #1 tags after filtering in treatment: 16385040 INFO @ Fri, 26 Jun 2020 23:03:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:03:08: #1 finished! INFO @ Fri, 26 Jun 2020 23:03:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:03:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:03:10: #2 number of paired peaks: 209 WARNING @ Fri, 26 Jun 2020 23:03:10: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 26 Jun 2020 23:03:10: start model_add_line... INFO @ Fri, 26 Jun 2020 23:03:10: start X-correlation... INFO @ Fri, 26 Jun 2020 23:03:10: end of X-cor INFO @ Fri, 26 Jun 2020 23:03:10: #2 finished! INFO @ Fri, 26 Jun 2020 23:03:10: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:03:10: #2 alternative fragment length(s) may be 1,11,35,109,563,586 bps INFO @ Fri, 26 Jun 2020 23:03:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.05_model.r WARNING @ Fri, 26 Jun 2020 23:03:10: #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 23:03:10: #2 You may need to consider one of the other alternative d(s): 1,11,35,109,563,586 WARNING @ Fri, 26 Jun 2020 23:03:10: #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 23:03:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:03:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:03:10: 7000000 INFO @ Fri, 26 Jun 2020 23:03:12: 12000000 INFO @ Fri, 26 Jun 2020 23:03:17: 8000000 INFO @ Fri, 26 Jun 2020 23:03:19: 13000000 INFO @ Fri, 26 Jun 2020 23:03:25: 9000000 INFO @ Fri, 26 Jun 2020 23:03:26: 14000000 INFO @ Fri, 26 Jun 2020 23:03:33: 10000000 INFO @ Fri, 26 Jun 2020 23:03:33: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:03:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:03:40: 16000000 INFO @ Fri, 26 Jun 2020 23:03:41: 11000000 INFO @ Fri, 26 Jun 2020 23:03:42: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:03:42: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:03:42: #1 total tags in treatment: 16385040 INFO @ Fri, 26 Jun 2020 23:03:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:03:42: #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 23:03:43: #1 tags after filtering in treatment: 16385040 INFO @ Fri, 26 Jun 2020 23:03:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:03:43: #1 finished! INFO @ Fri, 26 Jun 2020 23:03:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:03:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:03:44: #2 number of paired peaks: 209 WARNING @ Fri, 26 Jun 2020 23:03:44: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 26 Jun 2020 23:03:44: start model_add_line... INFO @ Fri, 26 Jun 2020 23:03:44: start X-correlation... INFO @ Fri, 26 Jun 2020 23:03:44: end of X-cor INFO @ Fri, 26 Jun 2020 23:03:44: #2 finished! INFO @ Fri, 26 Jun 2020 23:03:44: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:03:44: #2 alternative fragment length(s) may be 1,11,35,109,563,586 bps INFO @ Fri, 26 Jun 2020 23:03:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.10_model.r WARNING @ Fri, 26 Jun 2020 23:03:44: #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 23:03:44: #2 You may need to consider one of the other alternative d(s): 1,11,35,109,563,586 WARNING @ Fri, 26 Jun 2020 23:03:44: #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 23:03:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:03:48: 12000000 INFO @ Fri, 26 Jun 2020 23:03:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:03:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:03:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.05_summits.bed INFO @ Fri, 26 Jun 2020 23:03:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:03:55: 13000000 INFO @ Fri, 26 Jun 2020 23:04:02: 14000000 INFO @ Fri, 26 Jun 2020 23:04:09: 15000000 INFO @ Fri, 26 Jun 2020 23:04:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:04:16: 16000000 INFO @ Fri, 26 Jun 2020 23:04:19: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:04:19: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:04:19: #1 total tags in treatment: 16385040 INFO @ Fri, 26 Jun 2020 23:04:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:04:19: #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 23:04:19: #1 tags after filtering in treatment: 16385040 INFO @ Fri, 26 Jun 2020 23:04:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:04:19: #1 finished! INFO @ Fri, 26 Jun 2020 23:04:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:04:20: #2 number of paired peaks: 209 WARNING @ Fri, 26 Jun 2020 23:04:20: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 26 Jun 2020 23:04:20: start model_add_line... INFO @ Fri, 26 Jun 2020 23:04:21: start X-correlation... INFO @ Fri, 26 Jun 2020 23:04:21: end of X-cor INFO @ Fri, 26 Jun 2020 23:04:21: #2 finished! INFO @ Fri, 26 Jun 2020 23:04:21: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:04:21: #2 alternative fragment length(s) may be 1,11,35,109,563,586 bps INFO @ Fri, 26 Jun 2020 23:04:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.20_model.r WARNING @ Fri, 26 Jun 2020 23:04:21: #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 23:04:21: #2 You may need to consider one of the other alternative d(s): 1,11,35,109,563,586 WARNING @ Fri, 26 Jun 2020 23:04:21: #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 23:04:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:04:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.10_summits.bed INFO @ Fri, 26 Jun 2020 23:04:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:04:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:05:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:05:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:05:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494829/SRX494829.20_summits.bed INFO @ Fri, 26 Jun 2020 23:05:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling