Job ID = 6497437 SRX = SRX494935 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:10:50 prefetch.2.10.7: 1) Downloading 'SRR1198467'... 2020-06-25T22:10:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:15:51 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:15:51 prefetch.2.10.7: 1) 'SRR1198467' was downloaded successfully Read 32317902 spots for SRR1198467/SRR1198467.sra Written 32317902 spots for SRR1198467/SRR1198467.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: 00:07:20 32317902 reads; of these: 32317902 (100.00%) were unpaired; of these: 1920111 (5.94%) aligned 0 times 24974688 (77.28%) aligned exactly 1 time 5423103 (16.78%) aligned >1 times 94.06% overall alignment rate Time searching: 00:07:21 Overall time: 00:07:21 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] 5471654 / 30397791 = 0.1800 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 07:34:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.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 07:34:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:34:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:35:03: 1000000 INFO @ Fri, 26 Jun 2020 07:35:11: 2000000 INFO @ Fri, 26 Jun 2020 07:35:18: 3000000 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 07:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.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 07:35:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:35:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:35:26: 4000000 INFO @ Fri, 26 Jun 2020 07:35:34: 5000000 INFO @ Fri, 26 Jun 2020 07:35:34: 1000000 INFO @ Fri, 26 Jun 2020 07:35:42: 6000000 INFO @ Fri, 26 Jun 2020 07:35:43: 2000000 INFO @ Fri, 26 Jun 2020 07:35:50: 7000000 INFO @ Fri, 26 Jun 2020 07:35:52: 3000000 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 07:35:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.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 07:35:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:35:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:35:58: 8000000 INFO @ Fri, 26 Jun 2020 07:36:01: 4000000 INFO @ Fri, 26 Jun 2020 07:36:04: 1000000 INFO @ Fri, 26 Jun 2020 07:36:06: 9000000 INFO @ Fri, 26 Jun 2020 07:36:09: 5000000 INFO @ Fri, 26 Jun 2020 07:36:12: 2000000 INFO @ Fri, 26 Jun 2020 07:36:15: 10000000 INFO @ Fri, 26 Jun 2020 07:36:18: 6000000 INFO @ Fri, 26 Jun 2020 07:36:21: 3000000 INFO @ Fri, 26 Jun 2020 07:36:24: 11000000 INFO @ Fri, 26 Jun 2020 07:36:27: 7000000 INFO @ Fri, 26 Jun 2020 07:36:30: 4000000 INFO @ Fri, 26 Jun 2020 07:36:32: 12000000 INFO @ Fri, 26 Jun 2020 07:36:35: 8000000 INFO @ Fri, 26 Jun 2020 07:36:39: 5000000 INFO @ Fri, 26 Jun 2020 07:36:41: 13000000 INFO @ Fri, 26 Jun 2020 07:36:44: 9000000 INFO @ Fri, 26 Jun 2020 07:36:47: 6000000 INFO @ Fri, 26 Jun 2020 07:36:50: 14000000 INFO @ Fri, 26 Jun 2020 07:36:52: 10000000 INFO @ Fri, 26 Jun 2020 07:36:56: 7000000 INFO @ Fri, 26 Jun 2020 07:36:58: 15000000 INFO @ Fri, 26 Jun 2020 07:37:01: 11000000 INFO @ Fri, 26 Jun 2020 07:37:04: 8000000 INFO @ Fri, 26 Jun 2020 07:37:07: 16000000 INFO @ Fri, 26 Jun 2020 07:37:10: 12000000 INFO @ Fri, 26 Jun 2020 07:37:13: 9000000 INFO @ Fri, 26 Jun 2020 07:37:16: 17000000 INFO @ Fri, 26 Jun 2020 07:37:19: 13000000 INFO @ Fri, 26 Jun 2020 07:37:21: 10000000 INFO @ Fri, 26 Jun 2020 07:37:24: 18000000 INFO @ Fri, 26 Jun 2020 07:37:27: 14000000 INFO @ Fri, 26 Jun 2020 07:37:30: 11000000 INFO @ Fri, 26 Jun 2020 07:37:33: 19000000 INFO @ Fri, 26 Jun 2020 07:37:36: 15000000 INFO @ Fri, 26 Jun 2020 07:37:39: 12000000 INFO @ Fri, 26 Jun 2020 07:37:42: 20000000 INFO @ Fri, 26 Jun 2020 07:37:45: 16000000 INFO @ Fri, 26 Jun 2020 07:37:47: 13000000 INFO @ Fri, 26 Jun 2020 07:37:50: 21000000 INFO @ Fri, 26 Jun 2020 07:37:54: 17000000 INFO @ Fri, 26 Jun 2020 07:37:56: 14000000 INFO @ Fri, 26 Jun 2020 07:37:59: 22000000 INFO @ Fri, 26 Jun 2020 07:38:02: 18000000 INFO @ Fri, 26 Jun 2020 07:38:05: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:38:08: 23000000 INFO @ Fri, 26 Jun 2020 07:38:11: 19000000 INFO @ Fri, 26 Jun 2020 07:38:14: 16000000 INFO @ Fri, 26 Jun 2020 07:38:16: 24000000 INFO @ Fri, 26 Jun 2020 07:38:20: 20000000 INFO @ Fri, 26 Jun 2020 07:38:22: 17000000 INFO @ Fri, 26 Jun 2020 07:38:24: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:38:24: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:38:24: #1 total tags in treatment: 24926137 INFO @ Fri, 26 Jun 2020 07:38:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:38:24: #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 07:38:25: #1 tags after filtering in treatment: 24926137 INFO @ Fri, 26 Jun 2020 07:38:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:38:25: #1 finished! INFO @ Fri, 26 Jun 2020 07:38:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:38:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:38:26: #2 number of paired peaks: 127 WARNING @ Fri, 26 Jun 2020 07:38:26: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Fri, 26 Jun 2020 07:38:26: start model_add_line... INFO @ Fri, 26 Jun 2020 07:38:27: start X-correlation... INFO @ Fri, 26 Jun 2020 07:38:27: end of X-cor INFO @ Fri, 26 Jun 2020 07:38:27: #2 finished! INFO @ Fri, 26 Jun 2020 07:38:27: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:38:27: #2 alternative fragment length(s) may be 1,27 bps INFO @ Fri, 26 Jun 2020 07:38:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.05_model.r WARNING @ Fri, 26 Jun 2020 07:38:27: #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 07:38:27: #2 You may need to consider one of the other alternative d(s): 1,27 WARNING @ Fri, 26 Jun 2020 07:38:27: #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 07:38:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:38:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:38:29: 21000000 INFO @ Fri, 26 Jun 2020 07:38:30: 18000000 INFO @ Fri, 26 Jun 2020 07:38:37: 22000000 INFO @ Fri, 26 Jun 2020 07:38:38: 19000000 INFO @ Fri, 26 Jun 2020 07:38:46: 23000000 INFO @ Fri, 26 Jun 2020 07:38:46: 20000000 INFO @ Fri, 26 Jun 2020 07:38:54: 21000000 INFO @ Fri, 26 Jun 2020 07:38:55: 24000000 INFO @ Fri, 26 Jun 2020 07:39:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:39:02: 22000000 INFO @ Fri, 26 Jun 2020 07:39:03: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:39:03: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:39:03: #1 total tags in treatment: 24926137 INFO @ Fri, 26 Jun 2020 07:39:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:39:03: #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 07:39:04: #1 tags after filtering in treatment: 24926137 INFO @ Fri, 26 Jun 2020 07:39:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:39:04: #1 finished! INFO @ Fri, 26 Jun 2020 07:39:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:39:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:39:05: #2 number of paired peaks: 127 WARNING @ Fri, 26 Jun 2020 07:39:05: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Fri, 26 Jun 2020 07:39:05: start model_add_line... INFO @ Fri, 26 Jun 2020 07:39:05: start X-correlation... INFO @ Fri, 26 Jun 2020 07:39:05: end of X-cor INFO @ Fri, 26 Jun 2020 07:39:05: #2 finished! INFO @ Fri, 26 Jun 2020 07:39:05: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:39:05: #2 alternative fragment length(s) may be 1,27 bps INFO @ Fri, 26 Jun 2020 07:39:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.10_model.r WARNING @ Fri, 26 Jun 2020 07:39:05: #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 07:39:05: #2 You may need to consider one of the other alternative d(s): 1,27 WARNING @ Fri, 26 Jun 2020 07:39:05: #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 07:39:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:39:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:39:10: 23000000 INFO @ Fri, 26 Jun 2020 07:39:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:39:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:39:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.05_summits.bed INFO @ Fri, 26 Jun 2020 07:39:16: 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。 INFO @ Fri, 26 Jun 2020 07:39:18: 24000000 INFO @ Fri, 26 Jun 2020 07:39:25: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:39:25: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:39:25: #1 total tags in treatment: 24926137 INFO @ Fri, 26 Jun 2020 07:39:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:39:25: #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 07:39:26: #1 tags after filtering in treatment: 24926137 INFO @ Fri, 26 Jun 2020 07:39:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:39:26: #1 finished! INFO @ Fri, 26 Jun 2020 07:39:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:39:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:39:27: #2 number of paired peaks: 127 WARNING @ Fri, 26 Jun 2020 07:39:27: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Fri, 26 Jun 2020 07:39:27: start model_add_line... INFO @ Fri, 26 Jun 2020 07:39:28: start X-correlation... INFO @ Fri, 26 Jun 2020 07:39:28: end of X-cor INFO @ Fri, 26 Jun 2020 07:39:28: #2 finished! INFO @ Fri, 26 Jun 2020 07:39:28: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:39:28: #2 alternative fragment length(s) may be 1,27 bps INFO @ Fri, 26 Jun 2020 07:39:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.20_model.r WARNING @ Fri, 26 Jun 2020 07:39:28: #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 07:39:28: #2 You may need to consider one of the other alternative d(s): 1,27 WARNING @ Fri, 26 Jun 2020 07:39:28: #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 07:39:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:39:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:39:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:39:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:39:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:39:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.10_summits.bed INFO @ Fri, 26 Jun 2020 07:39:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:40:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:40:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:40:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:40:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494935/SRX494935.20_summits.bed INFO @ Fri, 26 Jun 2020 07:40:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling