Job ID = 6369009 SRX = SRX982075 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:40:14 prefetch.2.10.7: 1) Downloading 'SRR1956554'... 2020-06-16T00:40:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:41:51 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:41:52 prefetch.2.10.7: 'SRR1956554' is valid 2020-06-16T00:41:52 prefetch.2.10.7: 1) 'SRR1956554' was downloaded successfully Read 12102665 spots for SRR1956554/SRR1956554.sra Written 12102665 spots for SRR1956554/SRR1956554.sra 2020-06-16T00:42:37 prefetch.2.10.7: 1) Downloading 'SRR1956555'... 2020-06-16T00:42:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:45:12 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:45:13 prefetch.2.10.7: 'SRR1956555' is valid 2020-06-16T00:45:13 prefetch.2.10.7: 1) 'SRR1956555' was downloaded successfully Read 14224137 spots for SRR1956555/SRR1956555.sra Written 14224137 spots for SRR1956555/SRR1956555.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: 00:05:19 26326802 reads; of these: 26326802 (100.00%) were unpaired; of these: 1468631 (5.58%) aligned 0 times 20244968 (76.90%) aligned exactly 1 time 4613203 (17.52%) aligned >1 times 94.42% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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 12 files... [bam_rmdupse_core] 3768199 / 24858171 = 0.1516 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 09:57:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.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 09:57:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:57:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:57:45: 1000000 INFO @ Tue, 16 Jun 2020 09:57:52: 2000000 INFO @ Tue, 16 Jun 2020 09:57:59: 3000000 INFO @ Tue, 16 Jun 2020 09:58:05: 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 09:58:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.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 09:58:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:58:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:58:12: 5000000 INFO @ Tue, 16 Jun 2020 09:58:15: 1000000 INFO @ Tue, 16 Jun 2020 09:58:20: 6000000 INFO @ Tue, 16 Jun 2020 09:58:22: 2000000 INFO @ Tue, 16 Jun 2020 09:58:27: 7000000 INFO @ Tue, 16 Jun 2020 09:58:30: 3000000 INFO @ Tue, 16 Jun 2020 09:58:34: 8000000 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 09:58:37: 4000000 INFO @ Tue, 16 Jun 2020 09:58:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.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 09:58:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:58:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:58:41: 9000000 INFO @ Tue, 16 Jun 2020 09:58:44: 5000000 INFO @ Tue, 16 Jun 2020 09:58:45: 1000000 INFO @ Tue, 16 Jun 2020 09:58:49: 10000000 INFO @ Tue, 16 Jun 2020 09:58:52: 6000000 INFO @ Tue, 16 Jun 2020 09:58:53: 2000000 INFO @ Tue, 16 Jun 2020 09:58:56: 11000000 INFO @ Tue, 16 Jun 2020 09:58:59: 7000000 INFO @ Tue, 16 Jun 2020 09:59:00: 3000000 INFO @ Tue, 16 Jun 2020 09:59:04: 12000000 INFO @ Tue, 16 Jun 2020 09:59:07: 8000000 INFO @ Tue, 16 Jun 2020 09:59:08: 4000000 INFO @ Tue, 16 Jun 2020 09:59:11: 13000000 INFO @ Tue, 16 Jun 2020 09:59:14: 9000000 INFO @ Tue, 16 Jun 2020 09:59:15: 5000000 INFO @ Tue, 16 Jun 2020 09:59:19: 14000000 INFO @ Tue, 16 Jun 2020 09:59:21: 10000000 INFO @ Tue, 16 Jun 2020 09:59:23: 6000000 INFO @ Tue, 16 Jun 2020 09:59:26: 15000000 INFO @ Tue, 16 Jun 2020 09:59:29: 11000000 INFO @ Tue, 16 Jun 2020 09:59:30: 7000000 INFO @ Tue, 16 Jun 2020 09:59:33: 16000000 INFO @ Tue, 16 Jun 2020 09:59:36: 12000000 INFO @ Tue, 16 Jun 2020 09:59:38: 8000000 INFO @ Tue, 16 Jun 2020 09:59:41: 17000000 INFO @ Tue, 16 Jun 2020 09:59:44: 13000000 INFO @ Tue, 16 Jun 2020 09:59:45: 9000000 INFO @ Tue, 16 Jun 2020 09:59:49: 18000000 INFO @ Tue, 16 Jun 2020 09:59:51: 14000000 INFO @ Tue, 16 Jun 2020 09:59:53: 10000000 INFO @ Tue, 16 Jun 2020 09:59:56: 19000000 INFO @ Tue, 16 Jun 2020 09:59:58: 15000000 INFO @ Tue, 16 Jun 2020 10:00:00: 11000000 INFO @ Tue, 16 Jun 2020 10:00:04: 20000000 INFO @ Tue, 16 Jun 2020 10:00:05: 16000000 INFO @ Tue, 16 Jun 2020 10:00:08: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:00:11: 21000000 INFO @ Tue, 16 Jun 2020 10:00:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:00:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:00:12: #1 total tags in treatment: 21089972 INFO @ Tue, 16 Jun 2020 10:00:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:00:12: #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 10:00:12: #1 tags after filtering in treatment: 21089972 INFO @ Tue, 16 Jun 2020 10:00:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:00:12: #1 finished! INFO @ Tue, 16 Jun 2020 10:00:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:00:13: 17000000 INFO @ Tue, 16 Jun 2020 10:00:13: #2 number of paired peaks: 204 WARNING @ Tue, 16 Jun 2020 10:00:13: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 16 Jun 2020 10:00:13: start model_add_line... INFO @ Tue, 16 Jun 2020 10:00:14: start X-correlation... INFO @ Tue, 16 Jun 2020 10:00:14: end of X-cor INFO @ Tue, 16 Jun 2020 10:00:14: #2 finished! INFO @ Tue, 16 Jun 2020 10:00:14: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:00:14: #2 alternative fragment length(s) may be 1,30,588,597 bps INFO @ Tue, 16 Jun 2020 10:00:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.05_model.r WARNING @ Tue, 16 Jun 2020 10:00:14: #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 10:00:14: #2 You may need to consider one of the other alternative d(s): 1,30,588,597 WARNING @ Tue, 16 Jun 2020 10:00:14: #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 10:00:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:00:15: 13000000 INFO @ Tue, 16 Jun 2020 10:00:20: 18000000 INFO @ Tue, 16 Jun 2020 10:00:22: 14000000 INFO @ Tue, 16 Jun 2020 10:00:27: 19000000 INFO @ Tue, 16 Jun 2020 10:00:30: 15000000 INFO @ Tue, 16 Jun 2020 10:00:34: 20000000 INFO @ Tue, 16 Jun 2020 10:00:37: 16000000 INFO @ Tue, 16 Jun 2020 10:00:42: 21000000 INFO @ Tue, 16 Jun 2020 10:00:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:00:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:00:42: #1 total tags in treatment: 21089972 INFO @ Tue, 16 Jun 2020 10:00:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:00:42: #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 10:00:43: #1 tags after filtering in treatment: 21089972 INFO @ Tue, 16 Jun 2020 10:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:00:43: #1 finished! INFO @ Tue, 16 Jun 2020 10:00:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:00:44: #2 number of paired peaks: 204 WARNING @ Tue, 16 Jun 2020 10:00:44: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 16 Jun 2020 10:00:44: start model_add_line... INFO @ Tue, 16 Jun 2020 10:00:44: start X-correlation... INFO @ Tue, 16 Jun 2020 10:00:44: end of X-cor INFO @ Tue, 16 Jun 2020 10:00:44: #2 finished! INFO @ Tue, 16 Jun 2020 10:00:44: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:00:44: #2 alternative fragment length(s) may be 1,30,588,597 bps INFO @ Tue, 16 Jun 2020 10:00:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.10_model.r WARNING @ Tue, 16 Jun 2020 10:00:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:00:44: #2 You may need to consider one of the other alternative d(s): 1,30,588,597 WARNING @ Tue, 16 Jun 2020 10:00:44: #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 10:00:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:00:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:00:44: 17000000 INFO @ Tue, 16 Jun 2020 10:00:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:00:52: 18000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:00:59: 19000000 INFO @ Tue, 16 Jun 2020 10:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.05_summits.bed INFO @ Tue, 16 Jun 2020 10:01:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:01:06: 20000000 INFO @ Tue, 16 Jun 2020 10:01:13: 21000000 INFO @ Tue, 16 Jun 2020 10:01:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:01:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:01:13: #1 total tags in treatment: 21089972 INFO @ Tue, 16 Jun 2020 10:01:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:13: #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 10:01:14: #1 tags after filtering in treatment: 21089972 INFO @ Tue, 16 Jun 2020 10:01:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:01:14: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:15: #2 number of paired peaks: 204 WARNING @ Tue, 16 Jun 2020 10:01:15: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 16 Jun 2020 10:01:15: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:15: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:15: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:15: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:15: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:01:15: #2 alternative fragment length(s) may be 1,30,588,597 bps INFO @ Tue, 16 Jun 2020 10:01:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.20_model.r WARNING @ Tue, 16 Jun 2020 10:01:15: #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 10:01:15: #2 You may need to consider one of the other alternative d(s): 1,30,588,597 WARNING @ Tue, 16 Jun 2020 10:01:15: #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 10:01:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:01:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:01:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:01:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.10_summits.bed INFO @ Tue, 16 Jun 2020 10:01:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:01:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:02:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982075/SRX982075.20_summits.bed INFO @ Tue, 16 Jun 2020 10:02:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling