Job ID = 6367588 SRX = SRX331345 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:37:14 prefetch.2.10.7: 1) Downloading 'SRR947582'... 2020-06-15T23:37:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:52 prefetch.2.10.7: 1) 'SRR947582' was downloaded successfully Read 33231749 spots for SRR947582/SRR947582.sra Written 33231749 spots for SRR947582/SRR947582.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: 00:05:59 33231749 reads; of these: 33231749 (100.00%) were unpaired; of these: 356850 (1.07%) aligned 0 times 27446744 (82.59%) aligned exactly 1 time 5428155 (16.33%) aligned >1 times 98.93% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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 12 files... [bam_rmdupse_core] 7403810 / 32874899 = 0.2252 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 @ Tue, 16 Jun 2020 08:55:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.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 @ Tue, 16 Jun 2020 08:55:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:45: 1000000 INFO @ Tue, 16 Jun 2020 08:55:50: 2000000 INFO @ Tue, 16 Jun 2020 08:55:55: 3000000 INFO @ Tue, 16 Jun 2020 08:56:00: 4000000 INFO @ Tue, 16 Jun 2020 08:56:05: 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 @ Tue, 16 Jun 2020 08:56:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.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 @ Tue, 16 Jun 2020 08:56:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:10: 6000000 INFO @ Tue, 16 Jun 2020 08:56:15: 7000000 INFO @ Tue, 16 Jun 2020 08:56:15: 1000000 INFO @ Tue, 16 Jun 2020 08:56:21: 8000000 INFO @ Tue, 16 Jun 2020 08:56:21: 2000000 INFO @ Tue, 16 Jun 2020 08:56:26: 9000000 INFO @ Tue, 16 Jun 2020 08:56:26: 3000000 INFO @ Tue, 16 Jun 2020 08:56:31: 10000000 INFO @ Tue, 16 Jun 2020 08:56:31: 4000000 INFO @ Tue, 16 Jun 2020 08:56:36: 11000000 INFO @ Tue, 16 Jun 2020 08:56:37: 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 @ Tue, 16 Jun 2020 08:56:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.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 @ Tue, 16 Jun 2020 08:56:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:42: 12000000 INFO @ Tue, 16 Jun 2020 08:56:42: 6000000 INFO @ Tue, 16 Jun 2020 08:56:45: 1000000 INFO @ Tue, 16 Jun 2020 08:56:47: 13000000 INFO @ Tue, 16 Jun 2020 08:56:47: 7000000 INFO @ Tue, 16 Jun 2020 08:56:51: 2000000 INFO @ Tue, 16 Jun 2020 08:56:52: 14000000 INFO @ Tue, 16 Jun 2020 08:56:53: 8000000 INFO @ Tue, 16 Jun 2020 08:56:56: 3000000 INFO @ Tue, 16 Jun 2020 08:56:58: 15000000 INFO @ Tue, 16 Jun 2020 08:56:58: 9000000 INFO @ Tue, 16 Jun 2020 08:57:01: 4000000 INFO @ Tue, 16 Jun 2020 08:57:03: 16000000 INFO @ Tue, 16 Jun 2020 08:57:04: 10000000 INFO @ Tue, 16 Jun 2020 08:57:07: 5000000 INFO @ Tue, 16 Jun 2020 08:57:08: 17000000 INFO @ Tue, 16 Jun 2020 08:57:09: 11000000 INFO @ Tue, 16 Jun 2020 08:57:12: 6000000 INFO @ Tue, 16 Jun 2020 08:57:14: 18000000 INFO @ Tue, 16 Jun 2020 08:57:14: 12000000 INFO @ Tue, 16 Jun 2020 08:57:17: 7000000 INFO @ Tue, 16 Jun 2020 08:57:19: 19000000 INFO @ Tue, 16 Jun 2020 08:57:20: 13000000 INFO @ Tue, 16 Jun 2020 08:57:23: 8000000 INFO @ Tue, 16 Jun 2020 08:57:24: 20000000 INFO @ Tue, 16 Jun 2020 08:57:25: 14000000 INFO @ Tue, 16 Jun 2020 08:57:28: 9000000 INFO @ Tue, 16 Jun 2020 08:57:29: 21000000 INFO @ Tue, 16 Jun 2020 08:57:30: 15000000 INFO @ Tue, 16 Jun 2020 08:57:33: 10000000 INFO @ Tue, 16 Jun 2020 08:57:35: 22000000 INFO @ Tue, 16 Jun 2020 08:57:35: 16000000 INFO @ Tue, 16 Jun 2020 08:57:38: 11000000 INFO @ Tue, 16 Jun 2020 08:57:40: 23000000 INFO @ Tue, 16 Jun 2020 08:57:41: 17000000 INFO @ Tue, 16 Jun 2020 08:57:44: 12000000 INFO @ Tue, 16 Jun 2020 08:57:45: 24000000 INFO @ Tue, 16 Jun 2020 08:57:46: 18000000 INFO @ Tue, 16 Jun 2020 08:57:49: 13000000 INFO @ Tue, 16 Jun 2020 08:57:50: 25000000 INFO @ Tue, 16 Jun 2020 08:57:51: 19000000 INFO @ Tue, 16 Jun 2020 08:57:53: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:57:53: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:57:53: #1 total tags in treatment: 25471089 INFO @ Tue, 16 Jun 2020 08:57:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:57:53: #1 tags after filtering in treatment: 25471089 INFO @ Tue, 16 Jun 2020 08:57:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:54: 14000000 INFO @ Tue, 16 Jun 2020 08:57:55: #2 number of paired peaks: 153 WARNING @ Tue, 16 Jun 2020 08:57:55: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:55: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:57:55: #2 alternative fragment length(s) may be 1,35,109,326,355,429,467,495,509,530,569 bps INFO @ Tue, 16 Jun 2020 08:57:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.05_model.r WARNING @ Tue, 16 Jun 2020 08:57:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:55: #2 You may need to consider one of the other alternative d(s): 1,35,109,326,355,429,467,495,509,530,569 WARNING @ Tue, 16 Jun 2020 08:57:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:57:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:56: 20000000 INFO @ Tue, 16 Jun 2020 08:57:59: 15000000 INFO @ Tue, 16 Jun 2020 08:58:01: 21000000 INFO @ Tue, 16 Jun 2020 08:58:04: 16000000 INFO @ Tue, 16 Jun 2020 08:58:06: 22000000 INFO @ Tue, 16 Jun 2020 08:58:09: 17000000 INFO @ Tue, 16 Jun 2020 08:58:12: 23000000 INFO @ Tue, 16 Jun 2020 08:58:15: 18000000 INFO @ Tue, 16 Jun 2020 08:58:17: 24000000 INFO @ Tue, 16 Jun 2020 08:58:20: 19000000 INFO @ Tue, 16 Jun 2020 08:58:22: 25000000 INFO @ Tue, 16 Jun 2020 08:58:24: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:58:24: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:58:24: #1 total tags in treatment: 25471089 INFO @ Tue, 16 Jun 2020 08:58:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:58:25: 20000000 INFO @ Tue, 16 Jun 2020 08:58:25: #1 tags after filtering in treatment: 25471089 INFO @ Tue, 16 Jun 2020 08:58:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:27: #2 number of paired peaks: 153 WARNING @ Tue, 16 Jun 2020 08:58:27: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 16 Jun 2020 08:58:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:27: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:58:27: #2 alternative fragment length(s) may be 1,35,109,326,355,429,467,495,509,530,569 bps INFO @ Tue, 16 Jun 2020 08:58:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.10_model.r WARNING @ Tue, 16 Jun 2020 08:58:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:58:27: #2 You may need to consider one of the other alternative d(s): 1,35,109,326,355,429,467,495,509,530,569 WARNING @ Tue, 16 Jun 2020 08:58:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:58:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:27: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:58:30: 21000000 INFO @ Tue, 16 Jun 2020 08:58:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:35: 22000000 INFO @ Tue, 16 Jun 2020 08:58:40: 23000000 INFO @ Tue, 16 Jun 2020 08:58:44: 24000000 INFO @ Tue, 16 Jun 2020 08:58:49: 25000000 INFO @ Tue, 16 Jun 2020 08:58:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.05_summits.bed INFO @ Tue, 16 Jun 2020 08:58:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:52: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:58:52: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:58:52: #1 total tags in treatment: 25471089 INFO @ Tue, 16 Jun 2020 08:58:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:58:52: #1 tags after filtering in treatment: 25471089 INFO @ Tue, 16 Jun 2020 08:58:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:54: #2 number of paired peaks: 153 WARNING @ Tue, 16 Jun 2020 08:58:54: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 16 Jun 2020 08:58:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:54: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:58:54: #2 alternative fragment length(s) may be 1,35,109,326,355,429,467,495,509,530,569 bps INFO @ Tue, 16 Jun 2020 08:58:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.20_model.r WARNING @ Tue, 16 Jun 2020 08:58:54: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:58:54: #2 You may need to consider one of the other alternative d(s): 1,35,109,326,355,429,467,495,509,530,569 WARNING @ Tue, 16 Jun 2020 08:58:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:58:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.10_summits.bed INFO @ Tue, 16 Jun 2020 08:59:21: 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 @ Tue, 16 Jun 2020 08:59:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331345/SRX331345.20_summits.bed INFO @ Tue, 16 Jun 2020 08:59:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling