Job ID = 6497476 SRX = SRX494977 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:37:19 prefetch.2.10.7: 1) Downloading 'SRR1198509'... 2020-06-25T22:37:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:41:38 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:41:38 prefetch.2.10.7: 1) 'SRR1198509' was downloaded successfully Read 29285047 spots for SRR1198509/SRR1198509.sra Written 29285047 spots for SRR1198509/SRR1198509.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: 00:00:01 Multiseed full-index search: 00:06:55 29285047 reads; of these: 29285047 (100.00%) were unpaired; of these: 1130557 (3.86%) aligned 0 times 23737301 (81.06%) aligned exactly 1 time 4417189 (15.08%) aligned >1 times 96.14% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 11075664 / 28154490 = 0.3934 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 07:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.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 07:56:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:56:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:56:21: 1000000 INFO @ Fri, 26 Jun 2020 07:56:27: 2000000 INFO @ Fri, 26 Jun 2020 07:56:33: 3000000 INFO @ Fri, 26 Jun 2020 07:56:39: 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 07:56:45: 5000000 INFO @ Fri, 26 Jun 2020 07:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.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 07:56:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:56:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:56:52: 6000000 INFO @ Fri, 26 Jun 2020 07:56:52: 1000000 INFO @ Fri, 26 Jun 2020 07:56:58: 7000000 INFO @ Fri, 26 Jun 2020 07:56:59: 2000000 INFO @ Fri, 26 Jun 2020 07:57:05: 8000000 INFO @ Fri, 26 Jun 2020 07:57:06: 3000000 INFO @ Fri, 26 Jun 2020 07:57:12: 9000000 INFO @ Fri, 26 Jun 2020 07:57:12: 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 07:57:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.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 07:57:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:57:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:57:19: 10000000 INFO @ Fri, 26 Jun 2020 07:57:19: 5000000 INFO @ Fri, 26 Jun 2020 07:57:24: 1000000 INFO @ Fri, 26 Jun 2020 07:57:26: 11000000 INFO @ Fri, 26 Jun 2020 07:57:27: 6000000 INFO @ Fri, 26 Jun 2020 07:57:33: 2000000 INFO @ Fri, 26 Jun 2020 07:57:33: 12000000 INFO @ Fri, 26 Jun 2020 07:57:34: 7000000 INFO @ Fri, 26 Jun 2020 07:57:40: 13000000 INFO @ Fri, 26 Jun 2020 07:57:41: 3000000 INFO @ Fri, 26 Jun 2020 07:57:41: 8000000 INFO @ Fri, 26 Jun 2020 07:57:48: 14000000 INFO @ Fri, 26 Jun 2020 07:57:48: 9000000 INFO @ Fri, 26 Jun 2020 07:57:49: 4000000 INFO @ Fri, 26 Jun 2020 07:57:55: 15000000 INFO @ Fri, 26 Jun 2020 07:57:56: 10000000 INFO @ Fri, 26 Jun 2020 07:57:57: 5000000 INFO @ Fri, 26 Jun 2020 07:58:02: 16000000 INFO @ Fri, 26 Jun 2020 07:58:03: 11000000 INFO @ Fri, 26 Jun 2020 07:58:06: 6000000 INFO @ Fri, 26 Jun 2020 07:58:09: 17000000 INFO @ Fri, 26 Jun 2020 07:58:10: 12000000 INFO @ Fri, 26 Jun 2020 07:58:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:58:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:58:10: #1 total tags in treatment: 17078826 INFO @ Fri, 26 Jun 2020 07:58:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:58:10: #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 07:58:10: #1 tags after filtering in treatment: 17078826 INFO @ Fri, 26 Jun 2020 07:58:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:58:10: #1 finished! INFO @ Fri, 26 Jun 2020 07:58:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:58:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:58:12: #2 number of paired peaks: 191 WARNING @ Fri, 26 Jun 2020 07:58:12: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 26 Jun 2020 07:58:12: start model_add_line... INFO @ Fri, 26 Jun 2020 07:58:12: start X-correlation... INFO @ Fri, 26 Jun 2020 07:58:12: end of X-cor INFO @ Fri, 26 Jun 2020 07:58:12: #2 finished! INFO @ Fri, 26 Jun 2020 07:58:12: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:58:12: #2 alternative fragment length(s) may be 1,10,28,47,102,474,548 bps INFO @ Fri, 26 Jun 2020 07:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.05_model.r WARNING @ Fri, 26 Jun 2020 07:58:12: #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 07:58:12: #2 You may need to consider one of the other alternative d(s): 1,10,28,47,102,474,548 WARNING @ Fri, 26 Jun 2020 07:58:12: #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 07:58:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:58:14: 7000000 INFO @ Fri, 26 Jun 2020 07:58:17: 13000000 INFO @ Fri, 26 Jun 2020 07:58:22: 8000000 INFO @ Fri, 26 Jun 2020 07:58:24: 14000000 INFO @ Fri, 26 Jun 2020 07:58:30: 9000000 INFO @ Fri, 26 Jun 2020 07:58:31: 15000000 INFO @ Fri, 26 Jun 2020 07:58:38: 16000000 INFO @ Fri, 26 Jun 2020 07:58:38: 10000000 INFO @ Fri, 26 Jun 2020 07:58:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:58:45: 17000000 INFO @ Fri, 26 Jun 2020 07:58:45: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:58:45: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:58:45: #1 total tags in treatment: 17078826 INFO @ Fri, 26 Jun 2020 07:58:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:58:45: #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 07:58:46: #1 tags after filtering in treatment: 17078826 INFO @ Fri, 26 Jun 2020 07:58:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:58:46: #1 finished! INFO @ Fri, 26 Jun 2020 07:58:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:58:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:58:46: 11000000 INFO @ Fri, 26 Jun 2020 07:58:47: #2 number of paired peaks: 191 WARNING @ Fri, 26 Jun 2020 07:58:47: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 26 Jun 2020 07:58:47: start model_add_line... INFO @ Fri, 26 Jun 2020 07:58:47: start X-correlation... INFO @ Fri, 26 Jun 2020 07:58:47: end of X-cor INFO @ Fri, 26 Jun 2020 07:58:47: #2 finished! INFO @ Fri, 26 Jun 2020 07:58:47: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:58:47: #2 alternative fragment length(s) may be 1,10,28,47,102,474,548 bps INFO @ Fri, 26 Jun 2020 07:58:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.10_model.r WARNING @ Fri, 26 Jun 2020 07:58:47: #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 07:58:47: #2 You may need to consider one of the other alternative d(s): 1,10,28,47,102,474,548 WARNING @ Fri, 26 Jun 2020 07:58:47: #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 07:58:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:58:47: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:58:53: 12000000 INFO @ Fri, 26 Jun 2020 07:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.05_summits.bed INFO @ Fri, 26 Jun 2020 07:58:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:59:01: 13000000 INFO @ Fri, 26 Jun 2020 07:59:08: 14000000 INFO @ Fri, 26 Jun 2020 07:59:15: 15000000 INFO @ Fri, 26 Jun 2020 07:59:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:59:23: 16000000 INFO @ Fri, 26 Jun 2020 07:59:30: 17000000 INFO @ Fri, 26 Jun 2020 07:59:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:59:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:59:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.10_summits.bed INFO @ Fri, 26 Jun 2020 07:59:30: Done! INFO @ Fri, 26 Jun 2020 07:59:30: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:59:30: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:59:30: #1 total tags in treatment: 17078826 INFO @ Fri, 26 Jun 2020 07:59:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:59:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:59:31: #1 tags after filtering in treatment: 17078826 INFO @ Fri, 26 Jun 2020 07:59:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:59:31: #1 finished! INFO @ Fri, 26 Jun 2020 07:59:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:59:31: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:59:32: #2 number of paired peaks: 191 WARNING @ Fri, 26 Jun 2020 07:59:32: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 26 Jun 2020 07:59:32: start model_add_line... INFO @ Fri, 26 Jun 2020 07:59:32: start X-correlation... INFO @ Fri, 26 Jun 2020 07:59:32: end of X-cor INFO @ Fri, 26 Jun 2020 07:59:32: #2 finished! INFO @ Fri, 26 Jun 2020 07:59:32: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:59:32: #2 alternative fragment length(s) may be 1,10,28,47,102,474,548 bps INFO @ Fri, 26 Jun 2020 07:59:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.20_model.r WARNING @ Fri, 26 Jun 2020 07:59:32: #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 07:59:32: #2 You may need to consider one of the other alternative d(s): 1,10,28,47,102,474,548 WARNING @ Fri, 26 Jun 2020 07:59:32: #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 07:59:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:59:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:00:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:00:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494977/SRX494977.20_summits.bed INFO @ Fri, 26 Jun 2020 08:00:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling