Job ID = 6497400 SRX = SRX466519 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:45:01 prefetch.2.10.7: 1) Downloading 'SRR1163585'... 2020-06-25T21:45:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:46:45 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:46:45 prefetch.2.10.7: 1) 'SRR1163585' was downloaded successfully Read 30788149 spots for SRR1163585/SRR1163585.sra Written 30788149 spots for SRR1163585/SRR1163585.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: 00:05:06 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171811 (0.56%) aligned 0 times 25273583 (82.09%) aligned exactly 1 time 5342755 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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] 4711852 / 30616338 = 0.1539 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 06:59:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.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 06:59:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:59:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:00:01: 1000000 INFO @ Fri, 26 Jun 2020 07:00:06: 2000000 INFO @ Fri, 26 Jun 2020 07:00:12: 3000000 INFO @ Fri, 26 Jun 2020 07:00:17: 4000000 INFO @ Fri, 26 Jun 2020 07:00:23: 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 @ Fri, 26 Jun 2020 07:00:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.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 07:00:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:00:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:00:28: 6000000 INFO @ Fri, 26 Jun 2020 07:00:31: 1000000 INFO @ Fri, 26 Jun 2020 07:00:34: 7000000 INFO @ Fri, 26 Jun 2020 07:00:37: 2000000 INFO @ Fri, 26 Jun 2020 07:00:40: 8000000 INFO @ Fri, 26 Jun 2020 07:00:43: 3000000 INFO @ Fri, 26 Jun 2020 07:00:46: 9000000 INFO @ Fri, 26 Jun 2020 07:00:48: 4000000 INFO @ Fri, 26 Jun 2020 07:00:51: 10000000 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 07:00:54: 5000000 INFO @ Fri, 26 Jun 2020 07:00:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.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 07:00:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:00:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:00:57: 11000000 INFO @ Fri, 26 Jun 2020 07:01:00: 6000000 INFO @ Fri, 26 Jun 2020 07:01:01: 1000000 INFO @ Fri, 26 Jun 2020 07:01:03: 12000000 INFO @ Fri, 26 Jun 2020 07:01:06: 7000000 INFO @ Fri, 26 Jun 2020 07:01:07: 2000000 INFO @ Fri, 26 Jun 2020 07:01:09: 13000000 INFO @ Fri, 26 Jun 2020 07:01:12: 8000000 INFO @ Fri, 26 Jun 2020 07:01:13: 3000000 INFO @ Fri, 26 Jun 2020 07:01:15: 14000000 INFO @ Fri, 26 Jun 2020 07:01:18: 9000000 INFO @ Fri, 26 Jun 2020 07:01:19: 4000000 INFO @ Fri, 26 Jun 2020 07:01:20: 15000000 INFO @ Fri, 26 Jun 2020 07:01:23: 10000000 INFO @ Fri, 26 Jun 2020 07:01:25: 5000000 INFO @ Fri, 26 Jun 2020 07:01:26: 16000000 INFO @ Fri, 26 Jun 2020 07:01:29: 11000000 INFO @ Fri, 26 Jun 2020 07:01:31: 6000000 INFO @ Fri, 26 Jun 2020 07:01:32: 17000000 INFO @ Fri, 26 Jun 2020 07:01:35: 12000000 INFO @ Fri, 26 Jun 2020 07:01:37: 7000000 INFO @ Fri, 26 Jun 2020 07:01:38: 18000000 INFO @ Fri, 26 Jun 2020 07:01:41: 13000000 INFO @ Fri, 26 Jun 2020 07:01:42: 8000000 INFO @ Fri, 26 Jun 2020 07:01:44: 19000000 INFO @ Fri, 26 Jun 2020 07:01:47: 14000000 INFO @ Fri, 26 Jun 2020 07:01:48: 9000000 INFO @ Fri, 26 Jun 2020 07:01:50: 20000000 INFO @ Fri, 26 Jun 2020 07:01:53: 15000000 INFO @ Fri, 26 Jun 2020 07:01:54: 10000000 INFO @ Fri, 26 Jun 2020 07:01:56: 21000000 INFO @ Fri, 26 Jun 2020 07:01:59: 16000000 INFO @ Fri, 26 Jun 2020 07:02:00: 11000000 INFO @ Fri, 26 Jun 2020 07:02:02: 22000000 INFO @ Fri, 26 Jun 2020 07:02:05: 17000000 INFO @ Fri, 26 Jun 2020 07:02:06: 12000000 INFO @ Fri, 26 Jun 2020 07:02:08: 23000000 INFO @ Fri, 26 Jun 2020 07:02:12: 18000000 INFO @ Fri, 26 Jun 2020 07:02:12: 13000000 INFO @ Fri, 26 Jun 2020 07:02:14: 24000000 INFO @ Fri, 26 Jun 2020 07:02:18: 19000000 INFO @ Fri, 26 Jun 2020 07:02:18: 14000000 INFO @ Fri, 26 Jun 2020 07:02:20: 25000000 INFO @ Fri, 26 Jun 2020 07:02:24: 20000000 INFO @ Fri, 26 Jun 2020 07:02:24: 15000000 INFO @ Fri, 26 Jun 2020 07:02:25: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:02:25: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:02:25: #1 total tags in treatment: 25904486 INFO @ Fri, 26 Jun 2020 07:02:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:02:25: #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 07:02:26: #1 tags after filtering in treatment: 25904486 INFO @ Fri, 26 Jun 2020 07:02:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:02:26: #1 finished! INFO @ Fri, 26 Jun 2020 07:02:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:02:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:02:27: #2 number of paired peaks: 132 WARNING @ Fri, 26 Jun 2020 07:02:27: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 26 Jun 2020 07:02:27: start model_add_line... INFO @ Fri, 26 Jun 2020 07:02:27: start X-correlation... INFO @ Fri, 26 Jun 2020 07:02:27: end of X-cor INFO @ Fri, 26 Jun 2020 07:02:27: #2 finished! INFO @ Fri, 26 Jun 2020 07:02:27: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:02:27: #2 alternative fragment length(s) may be 1,33,251,299,382,535 bps INFO @ Fri, 26 Jun 2020 07:02:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.05_model.r WARNING @ Fri, 26 Jun 2020 07:02:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:02:27: #2 You may need to consider one of the other alternative d(s): 1,33,251,299,382,535 WARNING @ Fri, 26 Jun 2020 07:02:27: #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 07:02:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:02:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:02:30: 21000000 INFO @ Fri, 26 Jun 2020 07:02:31: 16000000 INFO @ Fri, 26 Jun 2020 07:02:36: 22000000 INFO @ Fri, 26 Jun 2020 07:02:37: 17000000 INFO @ Fri, 26 Jun 2020 07:02:42: 23000000 INFO @ Fri, 26 Jun 2020 07:02:43: 18000000 INFO @ Fri, 26 Jun 2020 07:02:48: 24000000 INFO @ Fri, 26 Jun 2020 07:02:49: 19000000 INFO @ Fri, 26 Jun 2020 07:02:54: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:02:55: 20000000 INFO @ Fri, 26 Jun 2020 07:02:59: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:02:59: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:02:59: #1 total tags in treatment: 25904486 INFO @ Fri, 26 Jun 2020 07:02:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:02:59: #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 07:02:59: #1 tags after filtering in treatment: 25904486 INFO @ Fri, 26 Jun 2020 07:02:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:02:59: #1 finished! INFO @ Fri, 26 Jun 2020 07:02:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:02:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:03:01: #2 number of paired peaks: 132 WARNING @ Fri, 26 Jun 2020 07:03:01: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 26 Jun 2020 07:03:01: start model_add_line... INFO @ Fri, 26 Jun 2020 07:03:01: start X-correlation... INFO @ Fri, 26 Jun 2020 07:03:01: end of X-cor INFO @ Fri, 26 Jun 2020 07:03:01: #2 finished! INFO @ Fri, 26 Jun 2020 07:03:01: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:03:01: #2 alternative fragment length(s) may be 1,33,251,299,382,535 bps INFO @ Fri, 26 Jun 2020 07:03:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.10_model.r INFO @ Fri, 26 Jun 2020 07:03:01: 21000000 INFO @ Fri, 26 Jun 2020 07:03:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:03:07: 22000000 WARNING @ Fri, 26 Jun 2020 07:03:11: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:03:11: #2 You may need to consider one of the other alternative d(s): 1,33,251,299,382,535 WARNING @ Fri, 26 Jun 2020 07:03:11: #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 07:03:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:03:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:03:13: 23000000 INFO @ Fri, 26 Jun 2020 07:03:19: 24000000 INFO @ Fri, 26 Jun 2020 07:03:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:03:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:03:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.05_summits.bed INFO @ Fri, 26 Jun 2020 07:03:20: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:03:24: 25000000 INFO @ Fri, 26 Jun 2020 07:03:29: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:03:29: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:03:29: #1 total tags in treatment: 25904486 INFO @ Fri, 26 Jun 2020 07:03:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:03:29: #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 07:03:30: #1 tags after filtering in treatment: 25904486 INFO @ Fri, 26 Jun 2020 07:03:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:03:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:03:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:03:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:03:31: #2 number of paired peaks: 132 WARNING @ Fri, 26 Jun 2020 07:03:31: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 26 Jun 2020 07:03:31: start model_add_line... INFO @ Fri, 26 Jun 2020 07:03:32: start X-correlation... INFO @ Fri, 26 Jun 2020 07:03:32: end of X-cor INFO @ Fri, 26 Jun 2020 07:03:32: #2 finished! INFO @ Fri, 26 Jun 2020 07:03:32: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:03:32: #2 alternative fragment length(s) may be 1,33,251,299,382,535 bps INFO @ Fri, 26 Jun 2020 07:03:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.20_model.r WARNING @ Fri, 26 Jun 2020 07:03:32: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:03:32: #2 You may need to consider one of the other alternative d(s): 1,33,251,299,382,535 WARNING @ Fri, 26 Jun 2020 07:03:32: #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 07:03:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:03:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:03:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:04:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:04:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.10_summits.bed INFO @ Fri, 26 Jun 2020 07:04:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:04:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:04:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:04:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:04:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466519/SRX466519.20_summits.bed INFO @ Fri, 26 Jun 2020 07:04:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling