Job ID = 6527417 SRX = SRX5402767 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:32:37 prefetch.2.10.7: 1) Downloading 'SRR8603001'... 2020-06-29T12:32:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:37:03 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:37:03 prefetch.2.10.7: 1) 'SRR8603001' was downloaded successfully Read 42012466 spots for SRR8603001/SRR8603001.sra Written 42012466 spots for SRR8603001/SRR8603001.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: 00:07:52 42012466 reads; of these: 42012466 (100.00%) were unpaired; of these: 9982107 (23.76%) aligned 0 times 25879966 (61.60%) aligned exactly 1 time 6150393 (14.64%) aligned >1 times 76.24% overall alignment rate Time searching: 00:07:52 Overall time: 00:07:52 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 16 files... [bam_rmdupse_core] 5244320 / 32030359 = 0.1637 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 22:02:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.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 22:02:22: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:02:22: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:02:27: 1000000 INFO @ Mon, 29 Jun 2020 22:02:32: 2000000 INFO @ Mon, 29 Jun 2020 22:02:38: 3000000 INFO @ Mon, 29 Jun 2020 22:02:43: 4000000 INFO @ Mon, 29 Jun 2020 22:02:48: 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 22:02:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.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 22:02:52: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:02:52: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:02:53: 6000000 INFO @ Mon, 29 Jun 2020 22:02:57: 1000000 INFO @ Mon, 29 Jun 2020 22:02:58: 7000000 INFO @ Mon, 29 Jun 2020 22:03:02: 2000000 INFO @ Mon, 29 Jun 2020 22:03:03: 8000000 INFO @ Mon, 29 Jun 2020 22:03:07: 3000000 INFO @ Mon, 29 Jun 2020 22:03:08: 9000000 INFO @ Mon, 29 Jun 2020 22:03:13: 4000000 INFO @ Mon, 29 Jun 2020 22:03:13: 10000000 INFO @ Mon, 29 Jun 2020 22:03:18: 5000000 INFO @ Mon, 29 Jun 2020 22:03:18: 11000000 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 22:03:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.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 22:03:22: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:03:22: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:03:23: 6000000 INFO @ Mon, 29 Jun 2020 22:03:23: 12000000 INFO @ Mon, 29 Jun 2020 22:03:28: 1000000 INFO @ Mon, 29 Jun 2020 22:03:29: 7000000 INFO @ Mon, 29 Jun 2020 22:03:29: 13000000 INFO @ Mon, 29 Jun 2020 22:03:34: 2000000 INFO @ Mon, 29 Jun 2020 22:03:35: 14000000 INFO @ Mon, 29 Jun 2020 22:03:35: 8000000 INFO @ Mon, 29 Jun 2020 22:03:39: 3000000 INFO @ Mon, 29 Jun 2020 22:03:40: 15000000 INFO @ Mon, 29 Jun 2020 22:03:40: 9000000 INFO @ Mon, 29 Jun 2020 22:03:45: 4000000 INFO @ Mon, 29 Jun 2020 22:03:46: 16000000 INFO @ Mon, 29 Jun 2020 22:03:46: 10000000 INFO @ Mon, 29 Jun 2020 22:03:51: 5000000 INFO @ Mon, 29 Jun 2020 22:03:51: 17000000 INFO @ Mon, 29 Jun 2020 22:03:52: 11000000 INFO @ Mon, 29 Jun 2020 22:03:57: 18000000 INFO @ Mon, 29 Jun 2020 22:03:57: 6000000 INFO @ Mon, 29 Jun 2020 22:03:58: 12000000 INFO @ Mon, 29 Jun 2020 22:04:02: 19000000 INFO @ Mon, 29 Jun 2020 22:04:03: 7000000 INFO @ Mon, 29 Jun 2020 22:04:03: 13000000 INFO @ Mon, 29 Jun 2020 22:04:08: 20000000 INFO @ Mon, 29 Jun 2020 22:04:08: 8000000 INFO @ Mon, 29 Jun 2020 22:04:09: 14000000 INFO @ Mon, 29 Jun 2020 22:04:13: 21000000 INFO @ Mon, 29 Jun 2020 22:04:14: 9000000 INFO @ Mon, 29 Jun 2020 22:04:15: 15000000 INFO @ Mon, 29 Jun 2020 22:04:18: 22000000 INFO @ Mon, 29 Jun 2020 22:04:20: 10000000 INFO @ Mon, 29 Jun 2020 22:04:20: 16000000 INFO @ Mon, 29 Jun 2020 22:04:24: 23000000 INFO @ Mon, 29 Jun 2020 22:04:25: 11000000 INFO @ Mon, 29 Jun 2020 22:04:26: 17000000 INFO @ Mon, 29 Jun 2020 22:04:29: 24000000 INFO @ Mon, 29 Jun 2020 22:04:31: 12000000 INFO @ Mon, 29 Jun 2020 22:04:32: 18000000 INFO @ Mon, 29 Jun 2020 22:04:35: 25000000 INFO @ Mon, 29 Jun 2020 22:04:37: 13000000 INFO @ Mon, 29 Jun 2020 22:04:37: 19000000 INFO @ Mon, 29 Jun 2020 22:04:40: 26000000 INFO @ Mon, 29 Jun 2020 22:04:42: 14000000 INFO @ Mon, 29 Jun 2020 22:04:43: 20000000 INFO @ Mon, 29 Jun 2020 22:04:45: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:04:45: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:04:45: #1 total tags in treatment: 26786039 INFO @ Mon, 29 Jun 2020 22:04:45: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:04:45: #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 22:04:45: #1 tags after filtering in treatment: 26786039 INFO @ Mon, 29 Jun 2020 22:04:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:04:45: #1 finished! INFO @ Mon, 29 Jun 2020 22:04:45: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:04:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:04:47: #2 number of paired peaks: 113 WARNING @ Mon, 29 Jun 2020 22:04:47: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 29 Jun 2020 22:04:47: start model_add_line... INFO @ Mon, 29 Jun 2020 22:04:47: start X-correlation... INFO @ Mon, 29 Jun 2020 22:04:47: end of X-cor INFO @ Mon, 29 Jun 2020 22:04:47: #2 finished! INFO @ Mon, 29 Jun 2020 22:04:47: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 22:04:47: #2 alternative fragment length(s) may be 1,43,581,598 bps INFO @ Mon, 29 Jun 2020 22:04:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.05_model.r WARNING @ Mon, 29 Jun 2020 22:04:47: #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 22:04:47: #2 You may need to consider one of the other alternative d(s): 1,43,581,598 WARNING @ Mon, 29 Jun 2020 22:04:47: #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 22:04:47: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:04:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:04:48: 15000000 INFO @ Mon, 29 Jun 2020 22:04:49: 21000000 INFO @ Mon, 29 Jun 2020 22:04:53: 16000000 INFO @ Mon, 29 Jun 2020 22:04:54: 22000000 INFO @ Mon, 29 Jun 2020 22:04:59: 17000000 INFO @ Mon, 29 Jun 2020 22:04:59: 23000000 INFO @ Mon, 29 Jun 2020 22:05:04: 18000000 INFO @ Mon, 29 Jun 2020 22:05:04: 24000000 INFO @ Mon, 29 Jun 2020 22:05:09: 19000000 INFO @ Mon, 29 Jun 2020 22:05:10: 25000000 INFO @ Mon, 29 Jun 2020 22:05:15: 20000000 INFO @ Mon, 29 Jun 2020 22:05:15: 26000000 INFO @ Mon, 29 Jun 2020 22:05:19: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:05:19: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:05:19: #1 total tags in treatment: 26786039 INFO @ Mon, 29 Jun 2020 22:05:19: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:05:19: #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 22:05:20: #1 tags after filtering in treatment: 26786039 INFO @ Mon, 29 Jun 2020 22:05:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:05:20: #1 finished! INFO @ Mon, 29 Jun 2020 22:05:20: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:05:20: 21000000 INFO @ Mon, 29 Jun 2020 22:05:21: #2 number of paired peaks: 113 WARNING @ Mon, 29 Jun 2020 22:05:21: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 29 Jun 2020 22:05:21: start model_add_line... INFO @ Mon, 29 Jun 2020 22:05:22: start X-correlation... INFO @ Mon, 29 Jun 2020 22:05:22: end of X-cor INFO @ Mon, 29 Jun 2020 22:05:22: #2 finished! INFO @ Mon, 29 Jun 2020 22:05:22: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 22:05:22: #2 alternative fragment length(s) may be 1,43,581,598 bps INFO @ Mon, 29 Jun 2020 22:05:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.10_model.r WARNING @ Mon, 29 Jun 2020 22:05:22: #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 22:05:22: #2 You may need to consider one of the other alternative d(s): 1,43,581,598 WARNING @ Mon, 29 Jun 2020 22:05:22: #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 22:05:22: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:05:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:05:25: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:05:25: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:05:30: 23000000 INFO @ Mon, 29 Jun 2020 22:05:35: 24000000 INFO @ Mon, 29 Jun 2020 22:05:40: 25000000 INFO @ Mon, 29 Jun 2020 22:05:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:05:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:05:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.05_summits.bed INFO @ Mon, 29 Jun 2020 22:05:42: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:05:45: 26000000 INFO @ Mon, 29 Jun 2020 22:05:49: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:05:49: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:05:49: #1 total tags in treatment: 26786039 INFO @ Mon, 29 Jun 2020 22:05:49: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:05:49: #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 22:05:49: #1 tags after filtering in treatment: 26786039 INFO @ Mon, 29 Jun 2020 22:05:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:05:49: #1 finished! INFO @ Mon, 29 Jun 2020 22:05:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:05:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:05:51: #2 number of paired peaks: 113 WARNING @ Mon, 29 Jun 2020 22:05:51: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 29 Jun 2020 22:05:51: start model_add_line... INFO @ Mon, 29 Jun 2020 22:05:51: start X-correlation... INFO @ Mon, 29 Jun 2020 22:05:51: end of X-cor INFO @ Mon, 29 Jun 2020 22:05:51: #2 finished! INFO @ Mon, 29 Jun 2020 22:05:51: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 22:05:51: #2 alternative fragment length(s) may be 1,43,581,598 bps INFO @ Mon, 29 Jun 2020 22:05:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.20_model.r WARNING @ Mon, 29 Jun 2020 22:05:51: #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 22:05:51: #2 You may need to consider one of the other alternative d(s): 1,43,581,598 WARNING @ Mon, 29 Jun 2020 22:05:51: #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 22:05:51: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:05:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:06:00: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:06:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:06:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:06:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.10_summits.bed INFO @ Mon, 29 Jun 2020 22:06:17: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:06:28: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:06:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:06:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:06:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402767/SRX5402767.20_summits.bed INFO @ Mon, 29 Jun 2020 22:06:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling