Job ID = 6366563 SRX = SRX1936241 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:08 prefetch.2.10.7: 1) Downloading 'SRR3879848'... 2020-06-15T23:05:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:41 prefetch.2.10.7: 1) 'SRR3879848' was downloaded successfully Read 21113861 spots for SRR3879848/SRR3879848.sra Written 21113861 spots for SRR3879848/SRR3879848.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: 00:05:04 21113861 reads; of these: 21113861 (100.00%) were unpaired; of these: 1032211 (4.89%) aligned 0 times 17122157 (81.09%) aligned exactly 1 time 2959493 (14.02%) aligned >1 times 95.11% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 2261075 / 20081650 = 0.1126 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 08:18:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.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 08:18:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:13: 1000000 INFO @ Tue, 16 Jun 2020 08:18:19: 2000000 INFO @ Tue, 16 Jun 2020 08:18:25: 3000000 INFO @ Tue, 16 Jun 2020 08:18:31: 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 08:18:37: 5000000 INFO @ Tue, 16 Jun 2020 08:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.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 08:18:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:43: 6000000 INFO @ Tue, 16 Jun 2020 08:18:44: 1000000 INFO @ Tue, 16 Jun 2020 08:18:49: 7000000 INFO @ Tue, 16 Jun 2020 08:18:50: 2000000 INFO @ Tue, 16 Jun 2020 08:18:56: 8000000 INFO @ Tue, 16 Jun 2020 08:18:57: 3000000 INFO @ Tue, 16 Jun 2020 08:19:02: 9000000 INFO @ Tue, 16 Jun 2020 08:19:03: 4000000 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 08:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.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 08:19:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:09: 10000000 INFO @ Tue, 16 Jun 2020 08:19:09: 5000000 INFO @ Tue, 16 Jun 2020 08:19:14: 1000000 INFO @ Tue, 16 Jun 2020 08:19:15: 11000000 INFO @ Tue, 16 Jun 2020 08:19:16: 6000000 INFO @ Tue, 16 Jun 2020 08:19:20: 2000000 INFO @ Tue, 16 Jun 2020 08:19:21: 12000000 INFO @ Tue, 16 Jun 2020 08:19:22: 7000000 INFO @ Tue, 16 Jun 2020 08:19:27: 3000000 INFO @ Tue, 16 Jun 2020 08:19:28: 13000000 INFO @ Tue, 16 Jun 2020 08:19:29: 8000000 INFO @ Tue, 16 Jun 2020 08:19:33: 4000000 INFO @ Tue, 16 Jun 2020 08:19:34: 14000000 INFO @ Tue, 16 Jun 2020 08:19:35: 9000000 INFO @ Tue, 16 Jun 2020 08:19:40: 5000000 INFO @ Tue, 16 Jun 2020 08:19:41: 15000000 INFO @ Tue, 16 Jun 2020 08:19:42: 10000000 INFO @ Tue, 16 Jun 2020 08:19:46: 6000000 INFO @ Tue, 16 Jun 2020 08:19:47: 16000000 INFO @ Tue, 16 Jun 2020 08:19:48: 11000000 INFO @ Tue, 16 Jun 2020 08:19:53: 7000000 INFO @ Tue, 16 Jun 2020 08:19:54: 17000000 INFO @ Tue, 16 Jun 2020 08:19:54: 12000000 INFO @ Tue, 16 Jun 2020 08:19:59: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:19:59: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:19:59: #1 total tags in treatment: 17820575 INFO @ Tue, 16 Jun 2020 08:19:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:59: #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 08:19:59: #1 tags after filtering in treatment: 17820575 INFO @ Tue, 16 Jun 2020 08:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:59: 8000000 INFO @ Tue, 16 Jun 2020 08:20:01: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 08:20:01: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:01: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:20:01: #2 alternative fragment length(s) may be 1,49,539,572,592 bps INFO @ Tue, 16 Jun 2020 08:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.05_model.r WARNING @ Tue, 16 Jun 2020 08:20:01: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:01: #2 You may need to consider one of the other alternative d(s): 1,49,539,572,592 WARNING @ Tue, 16 Jun 2020 08:20:01: #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 08:20:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:01: 13000000 INFO @ Tue, 16 Jun 2020 08:20:06: 9000000 INFO @ Tue, 16 Jun 2020 08:20:07: 14000000 INFO @ Tue, 16 Jun 2020 08:20:12: 10000000 INFO @ Tue, 16 Jun 2020 08:20:14: 15000000 INFO @ Tue, 16 Jun 2020 08:20:18: 11000000 INFO @ Tue, 16 Jun 2020 08:20:20: 16000000 INFO @ Tue, 16 Jun 2020 08:20:25: 12000000 INFO @ Tue, 16 Jun 2020 08:20:27: 17000000 INFO @ Tue, 16 Jun 2020 08:20:31: 13000000 INFO @ Tue, 16 Jun 2020 08:20:32: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:20:32: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:20:32: #1 total tags in treatment: 17820575 INFO @ Tue, 16 Jun 2020 08:20:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:32: #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 08:20:32: #1 tags after filtering in treatment: 17820575 INFO @ Tue, 16 Jun 2020 08:20:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:34: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 08:20:34: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:34: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:20:34: #2 alternative fragment length(s) may be 1,49,539,572,592 bps INFO @ Tue, 16 Jun 2020 08:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.10_model.r WARNING @ Tue, 16 Jun 2020 08:20:34: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:34: #2 You may need to consider one of the other alternative d(s): 1,49,539,572,592 WARNING @ Tue, 16 Jun 2020 08:20:34: #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 08:20:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:37: 14000000 INFO @ Tue, 16 Jun 2020 08:20:44: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:20:50: 16000000 INFO @ Tue, 16 Jun 2020 08:20:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (599 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:56: 17000000 INFO @ Tue, 16 Jun 2020 08:21:01: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:21:01: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:21:01: #1 total tags in treatment: 17820575 INFO @ Tue, 16 Jun 2020 08:21:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:01: #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 08:21:01: #1 tags after filtering in treatment: 17820575 INFO @ Tue, 16 Jun 2020 08:21:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:02: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 08:21:02: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:03: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:21:03: #2 alternative fragment length(s) may be 1,49,539,572,592 bps INFO @ Tue, 16 Jun 2020 08:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.20_model.r WARNING @ Tue, 16 Jun 2020 08:21:03: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:03: #2 You may need to consider one of the other alternative d(s): 1,49,539,572,592 WARNING @ Tue, 16 Jun 2020 08:21:03: #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 08:21:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.10_summits.bed INFO @ Tue, 16 Jun 2020 08:21:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936241/SRX1936241.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (135 records, 4 fields): 2 millis CompletedMACS2peakCalling