Job ID = 6497484 SRX = SRX495005 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:00:41 prefetch.2.10.7: 1) Downloading 'SRR1198537'... 2020-06-25T22:00:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:03:21 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:03:21 prefetch.2.10.7: 1) 'SRR1198537' was downloaded successfully Read 18057801 spots for SRR1198537/SRR1198537.sra Written 18057801 spots for SRR1198537/SRR1198537.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:25 18057801 reads; of these: 18057801 (100.00%) were unpaired; of these: 112888 (0.63%) aligned 0 times 15059336 (83.40%) aligned exactly 1 time 2885577 (15.98%) aligned >1 times 99.37% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 3188372 / 17944913 = 0.1777 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 07:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.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 07:12:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:12:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:13:01: 1000000 INFO @ Fri, 26 Jun 2020 07:13:05: 2000000 INFO @ Fri, 26 Jun 2020 07:13:10: 3000000 INFO @ Fri, 26 Jun 2020 07:13:14: 4000000 INFO @ Fri, 26 Jun 2020 07:13:19: 5000000 INFO @ Fri, 26 Jun 2020 07:13:23: 6000000 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 07:13:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.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 07:13:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:13:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:13:28: 7000000 INFO @ Fri, 26 Jun 2020 07:13:30: 1000000 INFO @ Fri, 26 Jun 2020 07:13:33: 8000000 INFO @ Fri, 26 Jun 2020 07:13:35: 2000000 INFO @ Fri, 26 Jun 2020 07:13:37: 9000000 INFO @ Fri, 26 Jun 2020 07:13:40: 3000000 INFO @ Fri, 26 Jun 2020 07:13:42: 10000000 INFO @ Fri, 26 Jun 2020 07:13:44: 4000000 INFO @ Fri, 26 Jun 2020 07:13:46: 11000000 INFO @ Fri, 26 Jun 2020 07:13:49: 5000000 INFO @ Fri, 26 Jun 2020 07:13:51: 12000000 INFO @ Fri, 26 Jun 2020 07:13:53: 6000000 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 07:13:56: 13000000 INFO @ Fri, 26 Jun 2020 07:13:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.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 07:13:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:13:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:13:58: 7000000 INFO @ Fri, 26 Jun 2020 07:14:00: 14000000 INFO @ Fri, 26 Jun 2020 07:14:01: 1000000 INFO @ Fri, 26 Jun 2020 07:14:02: 8000000 INFO @ Fri, 26 Jun 2020 07:14:04: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:14:04: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:14:04: #1 total tags in treatment: 14756541 INFO @ Fri, 26 Jun 2020 07:14:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:14:04: #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 07:14:04: #1 tags after filtering in treatment: 14756541 INFO @ Fri, 26 Jun 2020 07:14:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:14:04: #1 finished! INFO @ Fri, 26 Jun 2020 07:14:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:14:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:14:05: #2 number of paired peaks: 277 WARNING @ Fri, 26 Jun 2020 07:14:05: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Fri, 26 Jun 2020 07:14:05: start model_add_line... INFO @ Fri, 26 Jun 2020 07:14:05: start X-correlation... INFO @ Fri, 26 Jun 2020 07:14:05: end of X-cor INFO @ Fri, 26 Jun 2020 07:14:05: #2 finished! INFO @ Fri, 26 Jun 2020 07:14:05: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 07:14:05: #2 alternative fragment length(s) may be 1,40,555,574 bps INFO @ Fri, 26 Jun 2020 07:14:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.05_model.r WARNING @ Fri, 26 Jun 2020 07:14:05: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:14:05: #2 You may need to consider one of the other alternative d(s): 1,40,555,574 WARNING @ Fri, 26 Jun 2020 07:14:05: #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 07:14:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:14:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:14:06: 2000000 INFO @ Fri, 26 Jun 2020 07:14:07: 9000000 INFO @ Fri, 26 Jun 2020 07:14:10: 3000000 INFO @ Fri, 26 Jun 2020 07:14:11: 10000000 INFO @ Fri, 26 Jun 2020 07:14:15: 4000000 INFO @ Fri, 26 Jun 2020 07:14:16: 11000000 INFO @ Fri, 26 Jun 2020 07:14:20: 5000000 INFO @ Fri, 26 Jun 2020 07:14:21: 12000000 INFO @ Fri, 26 Jun 2020 07:14:24: 6000000 INFO @ Fri, 26 Jun 2020 07:14:25: 13000000 INFO @ Fri, 26 Jun 2020 07:14:29: 7000000 INFO @ Fri, 26 Jun 2020 07:14:30: 14000000 INFO @ Fri, 26 Jun 2020 07:14:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:14:34: 8000000 INFO @ Fri, 26 Jun 2020 07:14:34: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:14:34: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:14:34: #1 total tags in treatment: 14756541 INFO @ Fri, 26 Jun 2020 07:14:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:14:34: #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 07:14:34: #1 tags after filtering in treatment: 14756541 INFO @ Fri, 26 Jun 2020 07:14:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:14:34: #1 finished! INFO @ Fri, 26 Jun 2020 07:14:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:14:35: #2 number of paired peaks: 277 WARNING @ Fri, 26 Jun 2020 07:14:35: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Fri, 26 Jun 2020 07:14:35: start model_add_line... INFO @ Fri, 26 Jun 2020 07:14:35: start X-correlation... INFO @ Fri, 26 Jun 2020 07:14:35: end of X-cor INFO @ Fri, 26 Jun 2020 07:14:35: #2 finished! INFO @ Fri, 26 Jun 2020 07:14:35: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 07:14:35: #2 alternative fragment length(s) may be 1,40,555,574 bps INFO @ Fri, 26 Jun 2020 07:14:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.10_model.r INFO @ Fri, 26 Jun 2020 07:14:38: 9000000 WARNING @ Fri, 26 Jun 2020 07:14:41: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:14:41: #2 You may need to consider one of the other alternative d(s): 1,40,555,574 WARNING @ Fri, 26 Jun 2020 07:14:41: #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 07:14:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:14:43: 10000000 INFO @ Fri, 26 Jun 2020 07:14:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:14:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:14:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.05_summits.bed INFO @ Fri, 26 Jun 2020 07:14:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (690 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:14:47: 11000000 INFO @ Fri, 26 Jun 2020 07:14:52: 12000000 INFO @ Fri, 26 Jun 2020 07:14:56: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:15:01: 14000000 INFO @ Fri, 26 Jun 2020 07:15:04: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:15:04: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:15:04: #1 total tags in treatment: 14756541 INFO @ Fri, 26 Jun 2020 07:15:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:15:04: #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 07:15:05: #1 tags after filtering in treatment: 14756541 INFO @ Fri, 26 Jun 2020 07:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:15:05: #1 finished! INFO @ Fri, 26 Jun 2020 07:15:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:15:06: #2 number of paired peaks: 277 WARNING @ Fri, 26 Jun 2020 07:15:06: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Fri, 26 Jun 2020 07:15:06: start model_add_line... INFO @ Fri, 26 Jun 2020 07:15:06: start X-correlation... INFO @ Fri, 26 Jun 2020 07:15:06: end of X-cor INFO @ Fri, 26 Jun 2020 07:15:06: #2 finished! INFO @ Fri, 26 Jun 2020 07:15:06: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 07:15:06: #2 alternative fragment length(s) may be 1,40,555,574 bps INFO @ Fri, 26 Jun 2020 07:15:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.20_model.r WARNING @ Fri, 26 Jun 2020 07:15:06: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:15:06: #2 You may need to consider one of the other alternative d(s): 1,40,555,574 WARNING @ Fri, 26 Jun 2020 07:15:06: #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 07:15:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:15:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:15:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:15:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:15:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:15:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.10_summits.bed INFO @ Fri, 26 Jun 2020 07:15:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (301 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:15:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:15:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:15:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495005/SRX495005.20_summits.bed INFO @ Fri, 26 Jun 2020 07:15:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (99 records, 4 fields): 2 millis CompletedMACS2peakCalling