Job ID = 6367225 SRX = SRX3043411 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:19:01 prefetch.2.10.7: 1) Downloading 'SRR5875895'... 2020-06-15T23:19:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:20:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:20:54 prefetch.2.10.7: 1) 'SRR5875895' was downloaded successfully Read 18934290 spots for SRR5875895/SRR5875895.sra Written 18934290 spots for SRR5875895/SRR5875895.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: 00:05:12 18934290 reads; of these: 18934290 (100.00%) were unpaired; of these: 596294 (3.15%) aligned 0 times 15766885 (83.27%) aligned exactly 1 time 2571111 (13.58%) aligned >1 times 96.85% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 2582782 / 18337996 = 0.1408 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 08:32:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.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 08:32:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:28: 1000000 INFO @ Tue, 16 Jun 2020 08:32:34: 2000000 INFO @ Tue, 16 Jun 2020 08:32:40: 3000000 INFO @ Tue, 16 Jun 2020 08:32:45: 4000000 INFO @ Tue, 16 Jun 2020 08:32:51: 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 08:32:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.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 08:32:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:57: 6000000 INFO @ Tue, 16 Jun 2020 08:32:59: 1000000 INFO @ Tue, 16 Jun 2020 08:33:03: 7000000 INFO @ Tue, 16 Jun 2020 08:33:05: 2000000 INFO @ Tue, 16 Jun 2020 08:33:09: 8000000 INFO @ Tue, 16 Jun 2020 08:33:11: 3000000 INFO @ Tue, 16 Jun 2020 08:33:16: 9000000 INFO @ Tue, 16 Jun 2020 08:33:18: 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 08:33:22: 10000000 INFO @ Tue, 16 Jun 2020 08:33:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.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 08:33:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:24: 5000000 INFO @ Tue, 16 Jun 2020 08:33:28: 11000000 INFO @ Tue, 16 Jun 2020 08:33:30: 1000000 INFO @ Tue, 16 Jun 2020 08:33:30: 6000000 INFO @ Tue, 16 Jun 2020 08:33:34: 12000000 INFO @ Tue, 16 Jun 2020 08:33:36: 2000000 INFO @ Tue, 16 Jun 2020 08:33:37: 7000000 INFO @ Tue, 16 Jun 2020 08:33:41: 13000000 INFO @ Tue, 16 Jun 2020 08:33:42: 3000000 INFO @ Tue, 16 Jun 2020 08:33:43: 8000000 INFO @ Tue, 16 Jun 2020 08:33:47: 14000000 INFO @ Tue, 16 Jun 2020 08:33:49: 4000000 INFO @ Tue, 16 Jun 2020 08:33:49: 9000000 INFO @ Tue, 16 Jun 2020 08:33:53: 15000000 INFO @ Tue, 16 Jun 2020 08:33:55: 5000000 INFO @ Tue, 16 Jun 2020 08:33:56: 10000000 INFO @ Tue, 16 Jun 2020 08:33:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:33:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:33:58: #1 total tags in treatment: 15755214 INFO @ Tue, 16 Jun 2020 08:33:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:58: #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 08:33:58: #1 tags after filtering in treatment: 15755214 INFO @ Tue, 16 Jun 2020 08:33:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:59: #2 number of paired peaks: 118 WARNING @ Tue, 16 Jun 2020 08:33:59: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:59: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 08:33:59: #2 alternative fragment length(s) may be 1,55,117,154,210,355,382,461,472,562,591 bps INFO @ Tue, 16 Jun 2020 08:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.05_model.r WARNING @ Tue, 16 Jun 2020 08:33:59: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:59: #2 You may need to consider one of the other alternative d(s): 1,55,117,154,210,355,382,461,472,562,591 WARNING @ Tue, 16 Jun 2020 08:33:59: #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 08:33:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:01: 6000000 INFO @ Tue, 16 Jun 2020 08:34:02: 11000000 INFO @ Tue, 16 Jun 2020 08:34:08: 7000000 INFO @ Tue, 16 Jun 2020 08:34:08: 12000000 INFO @ Tue, 16 Jun 2020 08:34:14: 8000000 INFO @ Tue, 16 Jun 2020 08:34:15: 13000000 INFO @ Tue, 16 Jun 2020 08:34:20: 9000000 INFO @ Tue, 16 Jun 2020 08:34:21: 14000000 INFO @ Tue, 16 Jun 2020 08:34:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:26: 10000000 INFO @ Tue, 16 Jun 2020 08:34:27: 15000000 INFO @ Tue, 16 Jun 2020 08:34:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:34:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:34:32: #1 total tags in treatment: 15755214 INFO @ Tue, 16 Jun 2020 08:34:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:32: #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 08:34:32: #1 tags after filtering in treatment: 15755214 INFO @ Tue, 16 Jun 2020 08:34:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:33: 11000000 INFO @ Tue, 16 Jun 2020 08:34:33: #2 number of paired peaks: 118 WARNING @ Tue, 16 Jun 2020 08:34:33: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:33: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 08:34:33: #2 alternative fragment length(s) may be 1,55,117,154,210,355,382,461,472,562,591 bps INFO @ Tue, 16 Jun 2020 08:34:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.10_model.r WARNING @ Tue, 16 Jun 2020 08:34:33: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:33: #2 You may need to consider one of the other alternative d(s): 1,55,117,154,210,355,382,461,472,562,591 WARNING @ Tue, 16 Jun 2020 08:34:33: #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 08:34:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:39: 12000000 INFO @ Tue, 16 Jun 2020 08:34:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.05_summits.bed INFO @ Tue, 16 Jun 2020 08:34:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (507 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:45: 13000000 INFO @ Tue, 16 Jun 2020 08:34:50: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:34:56: 15000000 INFO @ Tue, 16 Jun 2020 08:35:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:35:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:35:01: #1 total tags in treatment: 15755214 INFO @ Tue, 16 Jun 2020 08:35:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:01: #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 08:35:01: #1 tags after filtering in treatment: 15755214 INFO @ Tue, 16 Jun 2020 08:35:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:02: #2 number of paired peaks: 118 WARNING @ Tue, 16 Jun 2020 08:35:02: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:02: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 08:35:02: #2 alternative fragment length(s) may be 1,55,117,154,210,355,382,461,472,562,591 bps INFO @ Tue, 16 Jun 2020 08:35:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.20_model.r WARNING @ Tue, 16 Jun 2020 08:35:02: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:35:02: #2 You may need to consider one of the other alternative d(s): 1,55,117,154,210,355,382,461,472,562,591 WARNING @ Tue, 16 Jun 2020 08:35:02: #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 08:35:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (274 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:35:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043411/SRX3043411.20_summits.bed INFO @ Tue, 16 Jun 2020 08:35:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (62 records, 4 fields): 1 millis CompletedMACS2peakCalling