Job ID = 6497433 SRX = SRX494931 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:04:19 prefetch.2.10.7: 1) Downloading 'SRR1198463'... 2020-06-25T22:04:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:05:53 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:05:53 prefetch.2.10.7: 1) 'SRR1198463' was downloaded successfully Read 15695316 spots for SRR1198463/SRR1198463.sra Written 15695316 spots for SRR1198463/SRR1198463.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: 00:03:27 15695316 reads; of these: 15695316 (100.00%) were unpaired; of these: 1827111 (11.64%) aligned 0 times 11334761 (72.22%) aligned exactly 1 time 2533444 (16.14%) aligned >1 times 88.36% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 1282240 / 13868205 = 0.0925 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 07:14:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.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 07:14:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:14:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:14:19: 1000000 INFO @ Fri, 26 Jun 2020 07:14:25: 2000000 INFO @ Fri, 26 Jun 2020 07:14:32: 3000000 INFO @ Fri, 26 Jun 2020 07:14:39: 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 07:14:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.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 07:14:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:14:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:14:46: 5000000 INFO @ Fri, 26 Jun 2020 07:14:49: 1000000 INFO @ Fri, 26 Jun 2020 07:14:53: 6000000 INFO @ Fri, 26 Jun 2020 07:14:56: 2000000 INFO @ Fri, 26 Jun 2020 07:15:00: 7000000 INFO @ Fri, 26 Jun 2020 07:15:03: 3000000 INFO @ Fri, 26 Jun 2020 07:15:07: 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 @ Fri, 26 Jun 2020 07:15:10: 4000000 INFO @ Fri, 26 Jun 2020 07:15:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.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 07:15:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:15:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:15:14: 9000000 INFO @ Fri, 26 Jun 2020 07:15:17: 5000000 INFO @ Fri, 26 Jun 2020 07:15:19: 1000000 INFO @ Fri, 26 Jun 2020 07:15:21: 10000000 INFO @ Fri, 26 Jun 2020 07:15:24: 6000000 INFO @ Fri, 26 Jun 2020 07:15:26: 2000000 INFO @ Fri, 26 Jun 2020 07:15:28: 11000000 INFO @ Fri, 26 Jun 2020 07:15:31: 7000000 INFO @ Fri, 26 Jun 2020 07:15:33: 3000000 INFO @ Fri, 26 Jun 2020 07:15:35: 12000000 INFO @ Fri, 26 Jun 2020 07:15:39: 8000000 INFO @ Fri, 26 Jun 2020 07:15:39: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:15:39: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:15:39: #1 total tags in treatment: 12585965 INFO @ Fri, 26 Jun 2020 07:15:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:15:39: #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 07:15:39: #1 tags after filtering in treatment: 12585965 INFO @ Fri, 26 Jun 2020 07:15:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:15:39: #1 finished! INFO @ Fri, 26 Jun 2020 07:15:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:15:40: #2 number of paired peaks: 348 WARNING @ Fri, 26 Jun 2020 07:15:40: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 26 Jun 2020 07:15:40: start model_add_line... INFO @ Fri, 26 Jun 2020 07:15:40: start X-correlation... INFO @ Fri, 26 Jun 2020 07:15:40: end of X-cor INFO @ Fri, 26 Jun 2020 07:15:40: #2 finished! INFO @ Fri, 26 Jun 2020 07:15:40: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 07:15:40: #2 alternative fragment length(s) may be 2,48,535,553 bps INFO @ Fri, 26 Jun 2020 07:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.05_model.r WARNING @ Fri, 26 Jun 2020 07:15:40: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:15:40: #2 You may need to consider one of the other alternative d(s): 2,48,535,553 WARNING @ Fri, 26 Jun 2020 07:15:40: #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 07:15:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:15:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:15:40: 4000000 INFO @ Fri, 26 Jun 2020 07:15:46: 9000000 INFO @ Fri, 26 Jun 2020 07:15:47: 5000000 INFO @ Fri, 26 Jun 2020 07:15:53: 10000000 INFO @ Fri, 26 Jun 2020 07:15:54: 6000000 INFO @ Fri, 26 Jun 2020 07:15:59: 11000000 INFO @ Fri, 26 Jun 2020 07:16:01: 7000000 INFO @ Fri, 26 Jun 2020 07:16:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:16:06: 12000000 INFO @ Fri, 26 Jun 2020 07:16:08: 8000000 INFO @ Fri, 26 Jun 2020 07:16:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:16:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:16:10: #1 total tags in treatment: 12585965 INFO @ Fri, 26 Jun 2020 07:16:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:16:10: #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 07:16:11: #1 tags after filtering in treatment: 12585965 INFO @ Fri, 26 Jun 2020 07:16:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:16:11: #1 finished! INFO @ Fri, 26 Jun 2020 07:16:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:16:11: #2 number of paired peaks: 348 WARNING @ Fri, 26 Jun 2020 07:16:11: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 26 Jun 2020 07:16:11: start model_add_line... INFO @ Fri, 26 Jun 2020 07:16:12: start X-correlation... INFO @ Fri, 26 Jun 2020 07:16:12: end of X-cor INFO @ Fri, 26 Jun 2020 07:16:12: #2 finished! INFO @ Fri, 26 Jun 2020 07:16:12: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 07:16:12: #2 alternative fragment length(s) may be 2,48,535,553 bps INFO @ Fri, 26 Jun 2020 07:16:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.10_model.r WARNING @ Fri, 26 Jun 2020 07:16:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:16:12: #2 You may need to consider one of the other alternative d(s): 2,48,535,553 WARNING @ Fri, 26 Jun 2020 07:16:12: #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 07:16:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:16:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:16:15: 9000000 INFO @ Fri, 26 Jun 2020 07:16:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.05_summits.bed INFO @ Fri, 26 Jun 2020 07:16:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (657 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:16:21: 10000000 INFO @ Fri, 26 Jun 2020 07:16:28: 11000000 INFO @ Fri, 26 Jun 2020 07:16:35: 12000000 INFO @ Fri, 26 Jun 2020 07:16:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:16:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:16:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:16:38: #1 total tags in treatment: 12585965 INFO @ Fri, 26 Jun 2020 07:16:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:16:38: #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 07:16:39: #1 tags after filtering in treatment: 12585965 INFO @ Fri, 26 Jun 2020 07:16:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:16:39: #1 finished! INFO @ Fri, 26 Jun 2020 07:16:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:16:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:16:39: #2 number of paired peaks: 348 WARNING @ Fri, 26 Jun 2020 07:16:39: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 26 Jun 2020 07:16:39: start model_add_line... INFO @ Fri, 26 Jun 2020 07:16:39: start X-correlation... INFO @ Fri, 26 Jun 2020 07:16:39: end of X-cor INFO @ Fri, 26 Jun 2020 07:16:39: #2 finished! INFO @ Fri, 26 Jun 2020 07:16:39: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 07:16:39: #2 alternative fragment length(s) may be 2,48,535,553 bps INFO @ Fri, 26 Jun 2020 07:16:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.20_model.r WARNING @ Fri, 26 Jun 2020 07:16:40: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:16:40: #2 You may need to consider one of the other alternative d(s): 2,48,535,553 WARNING @ Fri, 26 Jun 2020 07:16:40: #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 07:16:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:16:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.10_summits.bed INFO @ Fri, 26 Jun 2020 07:16:47: Done! BigWig に変換しました。 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:17:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:17:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:17:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:17:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494931/SRX494931.20_summits.bed INFO @ Fri, 26 Jun 2020 07:17:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 1 millis CompletedMACS2peakCalling