Job ID = 6366556 SRX = SRX1936234 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:50:56 prefetch.2.10.7: 1) Downloading 'SRR3879840'... 2020-06-15T22:50:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:52:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:52:14 prefetch.2.10.7: 1) 'SRR3879840' was downloaded successfully Read 19943258 spots for SRR3879840/SRR3879840.sra Written 19943258 spots for SRR3879840/SRR3879840.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: 00:04:52 19943258 reads; of these: 19943258 (100.00%) were unpaired; of these: 412736 (2.07%) aligned 0 times 16810289 (84.29%) aligned exactly 1 time 2720233 (13.64%) aligned >1 times 97.93% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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 8 files... [bam_rmdupse_core] 2377552 / 19530522 = 0.1217 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 08:03:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.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 08:03:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:27: 1000000 INFO @ Tue, 16 Jun 2020 08:03:33: 2000000 INFO @ Tue, 16 Jun 2020 08:03:39: 3000000 INFO @ Tue, 16 Jun 2020 08:03:45: 4000000 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 08:03:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.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 08:03:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:52: 5000000 INFO @ Tue, 16 Jun 2020 08:03:59: 1000000 INFO @ Tue, 16 Jun 2020 08:04:00: 6000000 INFO @ Tue, 16 Jun 2020 08:04:07: 2000000 INFO @ Tue, 16 Jun 2020 08:04:07: 7000000 INFO @ Tue, 16 Jun 2020 08:04:15: 8000000 INFO @ Tue, 16 Jun 2020 08:04:15: 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 @ Tue, 16 Jun 2020 08:04:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.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 08:04:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:23: 9000000 INFO @ Tue, 16 Jun 2020 08:04:24: 4000000 INFO @ Tue, 16 Jun 2020 08:04:28: 1000000 INFO @ Tue, 16 Jun 2020 08:04:30: 10000000 INFO @ Tue, 16 Jun 2020 08:04:33: 5000000 INFO @ Tue, 16 Jun 2020 08:04:36: 2000000 INFO @ Tue, 16 Jun 2020 08:04:38: 11000000 INFO @ Tue, 16 Jun 2020 08:04:41: 6000000 INFO @ Tue, 16 Jun 2020 08:04:44: 3000000 INFO @ Tue, 16 Jun 2020 08:04:46: 12000000 INFO @ Tue, 16 Jun 2020 08:04:50: 7000000 INFO @ Tue, 16 Jun 2020 08:04:52: 4000000 INFO @ Tue, 16 Jun 2020 08:04:54: 13000000 INFO @ Tue, 16 Jun 2020 08:04:58: 8000000 INFO @ Tue, 16 Jun 2020 08:05:00: 5000000 INFO @ Tue, 16 Jun 2020 08:05:02: 14000000 INFO @ Tue, 16 Jun 2020 08:05:07: 9000000 INFO @ Tue, 16 Jun 2020 08:05:08: 6000000 INFO @ Tue, 16 Jun 2020 08:05:10: 15000000 INFO @ Tue, 16 Jun 2020 08:05:16: 10000000 INFO @ Tue, 16 Jun 2020 08:05:16: 7000000 INFO @ Tue, 16 Jun 2020 08:05:18: 16000000 INFO @ Tue, 16 Jun 2020 08:05:24: 8000000 INFO @ Tue, 16 Jun 2020 08:05:25: 11000000 INFO @ Tue, 16 Jun 2020 08:05:26: 17000000 INFO @ Tue, 16 Jun 2020 08:05:28: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:05:28: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:05:28: #1 total tags in treatment: 17152970 INFO @ Tue, 16 Jun 2020 08:05:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:28: #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 08:05:28: #1 tags after filtering in treatment: 17152970 INFO @ Tue, 16 Jun 2020 08:05:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:29: #2 number of paired peaks: 100 WARNING @ Tue, 16 Jun 2020 08:05:29: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:29: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:05:29: #2 alternative fragment length(s) may be 1,52,514,534,557 bps INFO @ Tue, 16 Jun 2020 08:05:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.05_model.r WARNING @ Tue, 16 Jun 2020 08:05:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:29: #2 You may need to consider one of the other alternative d(s): 1,52,514,534,557 WARNING @ Tue, 16 Jun 2020 08:05:29: #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 08:05:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:32: 9000000 INFO @ Tue, 16 Jun 2020 08:05:33: 12000000 INFO @ Tue, 16 Jun 2020 08:05:40: 10000000 INFO @ Tue, 16 Jun 2020 08:05:42: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:05:47: 11000000 INFO @ Tue, 16 Jun 2020 08:05:51: 14000000 INFO @ Tue, 16 Jun 2020 08:05:55: 12000000 INFO @ Tue, 16 Jun 2020 08:05:59: 15000000 INFO @ Tue, 16 Jun 2020 08:06:03: 13000000 INFO @ Tue, 16 Jun 2020 08:06:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:08: 16000000 INFO @ Tue, 16 Jun 2020 08:06:11: 14000000 INFO @ Tue, 16 Jun 2020 08:06:17: 17000000 INFO @ Tue, 16 Jun 2020 08:06:18: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:06:18: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:06:18: #1 total tags in treatment: 17152970 INFO @ Tue, 16 Jun 2020 08:06:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:18: #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 08:06:18: 15000000 INFO @ Tue, 16 Jun 2020 08:06:18: #1 tags after filtering in treatment: 17152970 INFO @ Tue, 16 Jun 2020 08:06:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:20: #2 number of paired peaks: 100 WARNING @ Tue, 16 Jun 2020 08:06:20: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:20: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:06:20: #2 alternative fragment length(s) may be 1,52,514,534,557 bps INFO @ Tue, 16 Jun 2020 08:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.10_model.r WARNING @ Tue, 16 Jun 2020 08:06:20: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:20: #2 You may need to consider one of the other alternative d(s): 1,52,514,534,557 WARNING @ Tue, 16 Jun 2020 08:06:20: #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 08:06:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (544 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:25: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:06:32: 17000000 INFO @ Tue, 16 Jun 2020 08:06:33: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:06:33: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:06:33: #1 total tags in treatment: 17152970 INFO @ Tue, 16 Jun 2020 08:06:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:33: #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 08:06:34: #1 tags after filtering in treatment: 17152970 INFO @ Tue, 16 Jun 2020 08:06:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:35: #2 number of paired peaks: 100 WARNING @ Tue, 16 Jun 2020 08:06:35: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:35: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:06:35: #2 alternative fragment length(s) may be 1,52,514,534,557 bps INFO @ Tue, 16 Jun 2020 08:06:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.20_model.r WARNING @ Tue, 16 Jun 2020 08:06:35: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:35: #2 You may need to consider one of the other alternative d(s): 1,52,514,534,557 WARNING @ Tue, 16 Jun 2020 08:06:35: #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 08:06:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:12: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (313 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936234/SRX1936234.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (118 records, 4 fields): 2 millis CompletedMACS2peakCalling