Job ID = 6497452 SRX = SRX494949 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:36:04 prefetch.2.10.7: 1) Downloading 'SRR1198481'... 2020-06-25T22:36:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:37:33 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:37:34 prefetch.2.10.7: 'SRR1198481' is valid 2020-06-25T22:37:34 prefetch.2.10.7: 1) 'SRR1198481' was downloaded successfully Read 20769458 spots for SRR1198481/SRR1198481.sra Written 20769458 spots for SRR1198481/SRR1198481.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: 00:03:53 20769458 reads; of these: 20769458 (100.00%) were unpaired; of these: 277605 (1.34%) aligned 0 times 16888077 (81.31%) aligned exactly 1 time 3603776 (17.35%) aligned >1 times 98.66% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 2970412 / 20491853 = 0.1450 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 07:46:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.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 07:46:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:46:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:46:58: 1000000 INFO @ Fri, 26 Jun 2020 07:47:04: 2000000 INFO @ Fri, 26 Jun 2020 07:47:10: 3000000 INFO @ Fri, 26 Jun 2020 07:47:16: 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 07:47:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.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 07:47:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:47:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:47:22: 5000000 INFO @ Fri, 26 Jun 2020 07:47:28: 1000000 INFO @ Fri, 26 Jun 2020 07:47:29: 6000000 INFO @ Fri, 26 Jun 2020 07:47:34: 2000000 INFO @ Fri, 26 Jun 2020 07:47:36: 7000000 INFO @ Fri, 26 Jun 2020 07:47:41: 3000000 INFO @ Fri, 26 Jun 2020 07:47:42: 8000000 INFO @ Fri, 26 Jun 2020 07:47:47: 4000000 INFO @ Fri, 26 Jun 2020 07:47:49: 9000000 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 07:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.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 07:47:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:47:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:47:54: 5000000 INFO @ Fri, 26 Jun 2020 07:47:56: 10000000 INFO @ Fri, 26 Jun 2020 07:47:57: 1000000 INFO @ Fri, 26 Jun 2020 07:48:00: 6000000 INFO @ Fri, 26 Jun 2020 07:48:02: 11000000 INFO @ Fri, 26 Jun 2020 07:48:03: 2000000 INFO @ Fri, 26 Jun 2020 07:48:07: 7000000 INFO @ Fri, 26 Jun 2020 07:48:09: 12000000 INFO @ Fri, 26 Jun 2020 07:48:09: 3000000 INFO @ Fri, 26 Jun 2020 07:48:13: 8000000 INFO @ Fri, 26 Jun 2020 07:48:15: 13000000 INFO @ Fri, 26 Jun 2020 07:48:15: 4000000 INFO @ Fri, 26 Jun 2020 07:48:20: 9000000 INFO @ Fri, 26 Jun 2020 07:48:21: 5000000 INFO @ Fri, 26 Jun 2020 07:48:21: 14000000 INFO @ Fri, 26 Jun 2020 07:48:26: 10000000 INFO @ Fri, 26 Jun 2020 07:48:27: 6000000 INFO @ Fri, 26 Jun 2020 07:48:28: 15000000 INFO @ Fri, 26 Jun 2020 07:48:33: 11000000 INFO @ Fri, 26 Jun 2020 07:48:33: 7000000 INFO @ Fri, 26 Jun 2020 07:48:34: 16000000 INFO @ Fri, 26 Jun 2020 07:48:39: 12000000 INFO @ Fri, 26 Jun 2020 07:48:40: 8000000 INFO @ Fri, 26 Jun 2020 07:48:41: 17000000 INFO @ Fri, 26 Jun 2020 07:48:44: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:48:44: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:48:44: #1 total tags in treatment: 17521441 INFO @ Fri, 26 Jun 2020 07:48:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:48:44: #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 07:48:44: #1 tags after filtering in treatment: 17521441 INFO @ Fri, 26 Jun 2020 07:48:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:48:44: #1 finished! INFO @ Fri, 26 Jun 2020 07:48:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:48:45: 9000000 INFO @ Fri, 26 Jun 2020 07:48:46: #2 number of paired peaks: 261 WARNING @ Fri, 26 Jun 2020 07:48:46: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 26 Jun 2020 07:48:46: start model_add_line... INFO @ Fri, 26 Jun 2020 07:48:46: start X-correlation... INFO @ Fri, 26 Jun 2020 07:48:46: end of X-cor INFO @ Fri, 26 Jun 2020 07:48:46: #2 finished! INFO @ Fri, 26 Jun 2020 07:48:46: #2 predicted fragment length is 38 bps INFO @ Fri, 26 Jun 2020 07:48:46: #2 alternative fragment length(s) may be 2,38,71 bps INFO @ Fri, 26 Jun 2020 07:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.05_model.r WARNING @ Fri, 26 Jun 2020 07:48:46: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:48:46: #2 You may need to consider one of the other alternative d(s): 2,38,71 WARNING @ Fri, 26 Jun 2020 07:48:46: #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 07:48:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:48:46: 13000000 INFO @ Fri, 26 Jun 2020 07:48:51: 10000000 INFO @ Fri, 26 Jun 2020 07:48:52: 14000000 INFO @ Fri, 26 Jun 2020 07:48:57: 11000000 INFO @ Fri, 26 Jun 2020 07:48:58: 15000000 INFO @ Fri, 26 Jun 2020 07:49:03: 12000000 INFO @ Fri, 26 Jun 2020 07:49:05: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:49:09: 13000000 INFO @ Fri, 26 Jun 2020 07:49:11: 17000000 INFO @ Fri, 26 Jun 2020 07:49:14: 14000000 INFO @ Fri, 26 Jun 2020 07:49:14: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:49:14: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:49:14: #1 total tags in treatment: 17521441 INFO @ Fri, 26 Jun 2020 07:49:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:49:14: #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 07:49:15: #1 tags after filtering in treatment: 17521441 INFO @ Fri, 26 Jun 2020 07:49:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:49:15: #1 finished! INFO @ Fri, 26 Jun 2020 07:49:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:49:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:49:16: #2 number of paired peaks: 261 WARNING @ Fri, 26 Jun 2020 07:49:16: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 26 Jun 2020 07:49:16: start model_add_line... INFO @ Fri, 26 Jun 2020 07:49:16: start X-correlation... INFO @ Fri, 26 Jun 2020 07:49:16: end of X-cor INFO @ Fri, 26 Jun 2020 07:49:16: #2 finished! INFO @ Fri, 26 Jun 2020 07:49:16: #2 predicted fragment length is 38 bps INFO @ Fri, 26 Jun 2020 07:49:16: #2 alternative fragment length(s) may be 2,38,71 bps INFO @ Fri, 26 Jun 2020 07:49:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.10_model.r WARNING @ Fri, 26 Jun 2020 07:49:16: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:49:16: #2 You may need to consider one of the other alternative d(s): 2,38,71 WARNING @ Fri, 26 Jun 2020 07:49:16: #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 07:49:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:49:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:49:19: 15000000 INFO @ Fri, 26 Jun 2020 07:49:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:49:24: 16000000 INFO @ Fri, 26 Jun 2020 07:49:29: 17000000 INFO @ Fri, 26 Jun 2020 07:49:32: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:49:32: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:49:32: #1 total tags in treatment: 17521441 INFO @ Fri, 26 Jun 2020 07:49:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:49:32: #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 07:49:32: #1 tags after filtering in treatment: 17521441 INFO @ Fri, 26 Jun 2020 07:49:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:49:32: #1 finished! INFO @ Fri, 26 Jun 2020 07:49:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:49:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:49:33: #2 number of paired peaks: 261 WARNING @ Fri, 26 Jun 2020 07:49:33: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 26 Jun 2020 07:49:33: start model_add_line... INFO @ Fri, 26 Jun 2020 07:49:34: start X-correlation... INFO @ Fri, 26 Jun 2020 07:49:34: end of X-cor INFO @ Fri, 26 Jun 2020 07:49:34: #2 finished! INFO @ Fri, 26 Jun 2020 07:49:34: #2 predicted fragment length is 38 bps INFO @ Fri, 26 Jun 2020 07:49:34: #2 alternative fragment length(s) may be 2,38,71 bps INFO @ Fri, 26 Jun 2020 07:49:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.20_model.r WARNING @ Fri, 26 Jun 2020 07:49:34: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:49:34: #2 You may need to consider one of the other alternative d(s): 2,38,71 WARNING @ Fri, 26 Jun 2020 07:49:34: #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 07:49:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:49:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:49:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:49:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.05_summits.bed INFO @ Fri, 26 Jun 2020 07:49:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5315 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:49:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.10_summits.bed INFO @ Fri, 26 Jun 2020 07:50:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2498 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:50:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:50:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:50:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:50:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494949/SRX494949.20_summits.bed INFO @ Fri, 26 Jun 2020 07:50:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (552 records, 4 fields): 1 millis CompletedMACS2peakCalling