Job ID = 6497327 SRX = SRX059265 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:00:40 prefetch.2.10.7: 1) Downloading 'SRR190705'... 2020-06-25T22:00:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:02:28 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:02:29 prefetch.2.10.7: 'SRR190705' is valid 2020-06-25T22:02:29 prefetch.2.10.7: 1) 'SRR190705' was downloaded successfully Read 23070060 spots for SRR190705/SRR190705.sra Written 23070060 spots for SRR190705/SRR190705.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:16 23070060 reads; of these: 23070060 (100.00%) were unpaired; of these: 5700667 (24.71%) aligned 0 times 15029332 (65.15%) aligned exactly 1 time 2340061 (10.14%) aligned >1 times 75.29% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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] 2620698 / 17369393 = 0.1509 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 07:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.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 07:11:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:11:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:11:16: 1000000 INFO @ Fri, 26 Jun 2020 07:11:22: 2000000 INFO @ Fri, 26 Jun 2020 07:11:27: 3000000 INFO @ Fri, 26 Jun 2020 07:11:33: 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 07:11:39: 5000000 INFO @ Fri, 26 Jun 2020 07:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.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 07:11:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:11:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:11:45: 6000000 INFO @ Fri, 26 Jun 2020 07:11:47: 1000000 INFO @ Fri, 26 Jun 2020 07:11:51: 7000000 INFO @ Fri, 26 Jun 2020 07:11:53: 2000000 INFO @ Fri, 26 Jun 2020 07:11:57: 8000000 INFO @ Fri, 26 Jun 2020 07:11:59: 3000000 INFO @ Fri, 26 Jun 2020 07:12:03: 9000000 INFO @ Fri, 26 Jun 2020 07:12:06: 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 07:12:09: 10000000 INFO @ Fri, 26 Jun 2020 07:12:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.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 07:12:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:12:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:12:12: 5000000 INFO @ Fri, 26 Jun 2020 07:12:16: 11000000 INFO @ Fri, 26 Jun 2020 07:12:17: 1000000 INFO @ Fri, 26 Jun 2020 07:12:19: 6000000 INFO @ Fri, 26 Jun 2020 07:12:22: 12000000 INFO @ Fri, 26 Jun 2020 07:12:23: 2000000 INFO @ Fri, 26 Jun 2020 07:12:25: 7000000 INFO @ Fri, 26 Jun 2020 07:12:28: 13000000 INFO @ Fri, 26 Jun 2020 07:12:29: 3000000 INFO @ Fri, 26 Jun 2020 07:12:32: 8000000 INFO @ Fri, 26 Jun 2020 07:12:35: 14000000 INFO @ Fri, 26 Jun 2020 07:12:35: 4000000 INFO @ Fri, 26 Jun 2020 07:12:38: 9000000 INFO @ Fri, 26 Jun 2020 07:12:39: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:12:39: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:12:39: #1 total tags in treatment: 14748695 INFO @ Fri, 26 Jun 2020 07:12:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:12:39: #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 07:12:40: #1 tags after filtering in treatment: 14748695 INFO @ Fri, 26 Jun 2020 07:12:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:12:40: #1 finished! INFO @ Fri, 26 Jun 2020 07:12:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:12:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:12:41: #2 number of paired peaks: 149 WARNING @ Fri, 26 Jun 2020 07:12:41: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 26 Jun 2020 07:12:41: start model_add_line... INFO @ Fri, 26 Jun 2020 07:12:41: start X-correlation... INFO @ Fri, 26 Jun 2020 07:12:41: end of X-cor INFO @ Fri, 26 Jun 2020 07:12:41: #2 finished! INFO @ Fri, 26 Jun 2020 07:12:41: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 07:12:41: #2 alternative fragment length(s) may be 2,31,61,484,507,538,598 bps INFO @ Fri, 26 Jun 2020 07:12:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.05_model.r WARNING @ Fri, 26 Jun 2020 07:12:41: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:12:41: #2 You may need to consider one of the other alternative d(s): 2,31,61,484,507,538,598 WARNING @ Fri, 26 Jun 2020 07:12:41: #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 07:12:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:12:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:12:42: 5000000 INFO @ Fri, 26 Jun 2020 07:12:45: 10000000 INFO @ Fri, 26 Jun 2020 07:12:48: 6000000 INFO @ Fri, 26 Jun 2020 07:12:51: 11000000 INFO @ Fri, 26 Jun 2020 07:12:54: 7000000 INFO @ Fri, 26 Jun 2020 07:12:58: 12000000 INFO @ Fri, 26 Jun 2020 07:13:00: 8000000 INFO @ Fri, 26 Jun 2020 07:13:04: 13000000 INFO @ Fri, 26 Jun 2020 07:13:06: 9000000 INFO @ Fri, 26 Jun 2020 07:13:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:13:10: 14000000 INFO @ Fri, 26 Jun 2020 07:13:13: 10000000 INFO @ Fri, 26 Jun 2020 07:13:15: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:13:15: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:13:15: #1 total tags in treatment: 14748695 INFO @ Fri, 26 Jun 2020 07:13:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:13:15: #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 07:13:15: #1 tags after filtering in treatment: 14748695 INFO @ Fri, 26 Jun 2020 07:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:13:15: #1 finished! INFO @ Fri, 26 Jun 2020 07:13:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:13:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:13:16: #2 number of paired peaks: 149 WARNING @ Fri, 26 Jun 2020 07:13:16: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 26 Jun 2020 07:13:16: start model_add_line... INFO @ Fri, 26 Jun 2020 07:13:16: start X-correlation... INFO @ Fri, 26 Jun 2020 07:13:16: end of X-cor INFO @ Fri, 26 Jun 2020 07:13:16: #2 finished! INFO @ Fri, 26 Jun 2020 07:13:16: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 07:13:16: #2 alternative fragment length(s) may be 2,31,61,484,507,538,598 bps INFO @ Fri, 26 Jun 2020 07:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.10_model.r INFO @ Fri, 26 Jun 2020 07:13:18: 11000000 INFO @ Fri, 26 Jun 2020 07:13:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:13:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:13:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.05_summits.bed INFO @ Fri, 26 Jun 2020 07:13:23: Done! WARNING @ Fri, 26 Jun 2020 07:13:23: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:13:23: #2 You may need to consider one of the other alternative d(s): 2,31,61,484,507,538,598 WARNING @ Fri, 26 Jun 2020 07:13:23: #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 07:13:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:13:23: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:13:24: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:13:29: 13000000 INFO @ Fri, 26 Jun 2020 07:13:35: 14000000 INFO @ Fri, 26 Jun 2020 07:13:39: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:13:39: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:13:39: #1 total tags in treatment: 14748695 INFO @ Fri, 26 Jun 2020 07:13:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:13:39: #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 07:13:39: #1 tags after filtering in treatment: 14748695 INFO @ Fri, 26 Jun 2020 07:13:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:13:39: #1 finished! INFO @ Fri, 26 Jun 2020 07:13:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:13:40: #2 number of paired peaks: 149 WARNING @ Fri, 26 Jun 2020 07:13:40: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 26 Jun 2020 07:13:40: start model_add_line... INFO @ Fri, 26 Jun 2020 07:13:40: start X-correlation... INFO @ Fri, 26 Jun 2020 07:13:40: end of X-cor INFO @ Fri, 26 Jun 2020 07:13:40: #2 finished! INFO @ Fri, 26 Jun 2020 07:13:40: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 07:13:40: #2 alternative fragment length(s) may be 2,31,61,484,507,538,598 bps INFO @ Fri, 26 Jun 2020 07:13:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.20_model.r WARNING @ Fri, 26 Jun 2020 07:13:45: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:13:45: #2 You may need to consider one of the other alternative d(s): 2,31,61,484,507,538,598 WARNING @ Fri, 26 Jun 2020 07:13:45: #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 07:13:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:13:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:13:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.10_summits.bed INFO @ Fri, 26 Jun 2020 07:14:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:14:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:14:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:14:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:14:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059265/SRX059265.20_summits.bed INFO @ Fri, 26 Jun 2020 07:14:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling