Job ID = 6527399 SRX = SRX013987 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:12:16 prefetch.2.10.7: 1) Downloading 'SRR031093'... 2020-06-29T12:12:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:13:05 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:13:05 prefetch.2.10.7: 'SRR031093' is valid 2020-06-29T12:13:05 prefetch.2.10.7: 1) 'SRR031093' was downloaded successfully Read 6544503 spots for SRR031093/SRR031093.sra Written 6544503 spots for SRR031093/SRR031093.sra 2020-06-29T12:13:34 prefetch.2.10.7: 1) Downloading 'SRR031094'... 2020-06-29T12:13:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:14:22 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:14:23 prefetch.2.10.7: 'SRR031094' is valid 2020-06-29T12:14:23 prefetch.2.10.7: 1) 'SRR031094' was downloaded successfully Read 6460060 spots for SRR031094/SRR031094.sra Written 6460060 spots for SRR031094/SRR031094.sra 2020-06-29T12:14:52 prefetch.2.10.7: 1) Downloading 'SRR031095'... 2020-06-29T12:14:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:15:24 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:15:24 prefetch.2.10.7: 'SRR031095' is valid 2020-06-29T12:15:24 prefetch.2.10.7: 1) 'SRR031095' was downloaded successfully Read 6260093 spots for SRR031095/SRR031095.sra Written 6260093 spots for SRR031095/SRR031095.sra 2020-06-29T12:15:53 prefetch.2.10.7: 1) Downloading 'SRR031096'... 2020-06-29T12:15:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:16:30 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:16:30 prefetch.2.10.7: 'SRR031096' is valid 2020-06-29T12:16:30 prefetch.2.10.7: 1) 'SRR031096' was downloaded successfully Read 5759844 spots for SRR031096/SRR031096.sra Written 5759844 spots for SRR031096/SRR031096.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: 00:02:45 25024500 reads; of these: 25024500 (100.00%) were unpaired; of these: 7640383 (30.53%) aligned 0 times 14711812 (58.79%) aligned exactly 1 time 2672305 (10.68%) aligned >1 times 69.47% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 1630817 / 17384117 = 0.0938 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 @ Mon, 29 Jun 2020 21:28:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.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 @ Mon, 29 Jun 2020 21:28:25: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:28:25: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:28:30: 1000000 INFO @ Mon, 29 Jun 2020 21:28:35: 2000000 INFO @ Mon, 29 Jun 2020 21:28:40: 3000000 INFO @ Mon, 29 Jun 2020 21:28:45: 4000000 INFO @ Mon, 29 Jun 2020 21:28:49: 5000000 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 @ Mon, 29 Jun 2020 21:28:54: 6000000 INFO @ Mon, 29 Jun 2020 21:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.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 @ Mon, 29 Jun 2020 21:28:55: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:28:55: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:28:59: 7000000 INFO @ Mon, 29 Jun 2020 21:29:01: 1000000 INFO @ Mon, 29 Jun 2020 21:29:05: 8000000 INFO @ Mon, 29 Jun 2020 21:29:06: 2000000 INFO @ Mon, 29 Jun 2020 21:29:10: 9000000 INFO @ Mon, 29 Jun 2020 21:29:11: 3000000 INFO @ Mon, 29 Jun 2020 21:29:15: 10000000 INFO @ Mon, 29 Jun 2020 21:29:16: 4000000 INFO @ Mon, 29 Jun 2020 21:29:21: 11000000 INFO @ Mon, 29 Jun 2020 21:29:21: 5000000 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 @ Mon, 29 Jun 2020 21:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.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 @ Mon, 29 Jun 2020 21:29:25: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:29:25: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:29:26: 12000000 INFO @ Mon, 29 Jun 2020 21:29:27: 6000000 INFO @ Mon, 29 Jun 2020 21:29:30: 1000000 INFO @ Mon, 29 Jun 2020 21:29:32: 13000000 INFO @ Mon, 29 Jun 2020 21:29:32: 7000000 INFO @ Mon, 29 Jun 2020 21:29:35: 2000000 INFO @ Mon, 29 Jun 2020 21:29:37: 14000000 INFO @ Mon, 29 Jun 2020 21:29:38: 8000000 INFO @ Mon, 29 Jun 2020 21:29:40: 3000000 INFO @ Mon, 29 Jun 2020 21:29:43: 15000000 INFO @ Mon, 29 Jun 2020 21:29:43: 9000000 INFO @ Mon, 29 Jun 2020 21:29:45: 4000000 INFO @ Mon, 29 Jun 2020 21:29:47: #1 tag size is determined as 27 bps INFO @ Mon, 29 Jun 2020 21:29:47: #1 tag size = 27 INFO @ Mon, 29 Jun 2020 21:29:47: #1 total tags in treatment: 15753300 INFO @ Mon, 29 Jun 2020 21:29:47: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:29:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:29:47: #1 tags after filtering in treatment: 15753300 INFO @ Mon, 29 Jun 2020 21:29:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:29:47: #1 finished! INFO @ Mon, 29 Jun 2020 21:29:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:29:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:29:48: #2 number of paired peaks: 216 WARNING @ Mon, 29 Jun 2020 21:29:48: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Mon, 29 Jun 2020 21:29:48: start model_add_line... INFO @ Mon, 29 Jun 2020 21:29:48: start X-correlation... INFO @ Mon, 29 Jun 2020 21:29:48: end of X-cor INFO @ Mon, 29 Jun 2020 21:29:48: #2 finished! INFO @ Mon, 29 Jun 2020 21:29:48: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:29:48: #2 alternative fragment length(s) may be 1,24,71,593 bps INFO @ Mon, 29 Jun 2020 21:29:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.05_model.r WARNING @ Mon, 29 Jun 2020 21:29:48: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:29:48: #2 You may need to consider one of the other alternative d(s): 1,24,71,593 WARNING @ Mon, 29 Jun 2020 21:29:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:29:48: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:29:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:29:48: 10000000 INFO @ Mon, 29 Jun 2020 21:29:49: 5000000 INFO @ Mon, 29 Jun 2020 21:29:54: 11000000 INFO @ Mon, 29 Jun 2020 21:29:54: 6000000 INFO @ Mon, 29 Jun 2020 21:29:59: 12000000 INFO @ Mon, 29 Jun 2020 21:29:59: 7000000 INFO @ Mon, 29 Jun 2020 21:30:04: 8000000 INFO @ Mon, 29 Jun 2020 21:30:04: 13000000 INFO @ Mon, 29 Jun 2020 21:30:09: 9000000 INFO @ Mon, 29 Jun 2020 21:30:09: 14000000 INFO @ Mon, 29 Jun 2020 21:30:12: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:30:13: 10000000 INFO @ Mon, 29 Jun 2020 21:30:14: 15000000 INFO @ Mon, 29 Jun 2020 21:30:18: #1 tag size is determined as 27 bps INFO @ Mon, 29 Jun 2020 21:30:18: #1 tag size = 27 INFO @ Mon, 29 Jun 2020 21:30:18: #1 total tags in treatment: 15753300 INFO @ Mon, 29 Jun 2020 21:30:18: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:30:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:30:18: 11000000 INFO @ Mon, 29 Jun 2020 21:30:18: #1 tags after filtering in treatment: 15753300 INFO @ Mon, 29 Jun 2020 21:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:30:18: #1 finished! INFO @ Mon, 29 Jun 2020 21:30:18: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:30:19: #2 number of paired peaks: 216 WARNING @ Mon, 29 Jun 2020 21:30:19: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Mon, 29 Jun 2020 21:30:19: start model_add_line... INFO @ Mon, 29 Jun 2020 21:30:19: start X-correlation... INFO @ Mon, 29 Jun 2020 21:30:19: end of X-cor INFO @ Mon, 29 Jun 2020 21:30:19: #2 finished! INFO @ Mon, 29 Jun 2020 21:30:19: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:30:19: #2 alternative fragment length(s) may be 1,24,71,593 bps INFO @ Mon, 29 Jun 2020 21:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.10_model.r WARNING @ Mon, 29 Jun 2020 21:30:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:30:20: #2 You may need to consider one of the other alternative d(s): 1,24,71,593 WARNING @ Mon, 29 Jun 2020 21:30:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:30:20: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:30:23: 12000000 INFO @ Mon, 29 Jun 2020 21:30:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:30:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:30:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.05_summits.bed INFO @ Mon, 29 Jun 2020 21:30:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:30:27: 13000000 INFO @ Mon, 29 Jun 2020 21:30:32: 14000000 INFO @ Mon, 29 Jun 2020 21:30:36: 15000000 INFO @ Mon, 29 Jun 2020 21:30:40: #1 tag size is determined as 27 bps INFO @ Mon, 29 Jun 2020 21:30:40: #1 tag size = 27 INFO @ Mon, 29 Jun 2020 21:30:40: #1 total tags in treatment: 15753300 INFO @ Mon, 29 Jun 2020 21:30:40: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:30:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:30:40: #1 tags after filtering in treatment: 15753300 INFO @ Mon, 29 Jun 2020 21:30:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:30:40: #1 finished! INFO @ Mon, 29 Jun 2020 21:30:40: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:30:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:30:41: #2 number of paired peaks: 216 WARNING @ Mon, 29 Jun 2020 21:30:41: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Mon, 29 Jun 2020 21:30:41: start model_add_line... INFO @ Mon, 29 Jun 2020 21:30:42: start X-correlation... INFO @ Mon, 29 Jun 2020 21:30:42: end of X-cor INFO @ Mon, 29 Jun 2020 21:30:42: #2 finished! INFO @ Mon, 29 Jun 2020 21:30:42: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:30:42: #2 alternative fragment length(s) may be 1,24,71,593 bps INFO @ Mon, 29 Jun 2020 21:30:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.20_model.r WARNING @ Mon, 29 Jun 2020 21:30:42: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:30:42: #2 You may need to consider one of the other alternative d(s): 1,24,71,593 WARNING @ Mon, 29 Jun 2020 21:30:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:30:42: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:30:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:30:43: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:30:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:30:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:30:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.10_summits.bed INFO @ Mon, 29 Jun 2020 21:30:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:31:05: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:31:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:31:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:31:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX013987/SRX013987.20_summits.bed INFO @ Mon, 29 Jun 2020 21:31:16: 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。