Job ID = 6527406 SRX = SRX3043410 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:11:46 prefetch.2.10.7: 1) Downloading 'SRR5875894'... 2020-06-29T12:11:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:15:13 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:15:13 prefetch.2.10.7: 1) 'SRR5875894' was downloaded successfully Read 17754014 spots for SRR5875894/SRR5875894.sra Written 17754014 spots for SRR5875894/SRR5875894.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: 00:05:23 17754014 reads; of these: 17754014 (100.00%) were unpaired; of these: 406200 (2.29%) aligned 0 times 14871300 (83.76%) aligned exactly 1 time 2476514 (13.95%) aligned >1 times 97.71% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 2364853 / 17347814 = 0.1363 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 @ Mon, 29 Jun 2020 21:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.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 @ Mon, 29 Jun 2020 21:33:05: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:33:05: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:33:11: 1000000 INFO @ Mon, 29 Jun 2020 21:33:18: 2000000 INFO @ Mon, 29 Jun 2020 21:33:24: 3000000 INFO @ Mon, 29 Jun 2020 21:33:31: 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 @ Mon, 29 Jun 2020 21:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.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 @ Mon, 29 Jun 2020 21:33:35: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:33:35: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:33:37: 5000000 INFO @ Mon, 29 Jun 2020 21:33:43: 1000000 INFO @ Mon, 29 Jun 2020 21:33:44: 6000000 INFO @ Mon, 29 Jun 2020 21:33:50: 7000000 INFO @ Mon, 29 Jun 2020 21:33:50: 2000000 INFO @ Mon, 29 Jun 2020 21:33:57: 8000000 INFO @ Mon, 29 Jun 2020 21:33:57: 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 @ Mon, 29 Jun 2020 21:34:04: 9000000 INFO @ Mon, 29 Jun 2020 21:34:04: 4000000 INFO @ Mon, 29 Jun 2020 21:34:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.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 @ Mon, 29 Jun 2020 21:34:05: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:34:05: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:34:10: 10000000 INFO @ Mon, 29 Jun 2020 21:34:11: 5000000 INFO @ Mon, 29 Jun 2020 21:34:12: 1000000 INFO @ Mon, 29 Jun 2020 21:34:17: 11000000 INFO @ Mon, 29 Jun 2020 21:34:19: 6000000 INFO @ Mon, 29 Jun 2020 21:34:20: 2000000 INFO @ Mon, 29 Jun 2020 21:34:23: 12000000 INFO @ Mon, 29 Jun 2020 21:34:26: 7000000 INFO @ Mon, 29 Jun 2020 21:34:27: 3000000 INFO @ Mon, 29 Jun 2020 21:34:29: 13000000 INFO @ Mon, 29 Jun 2020 21:34:34: 8000000 INFO @ Mon, 29 Jun 2020 21:34:35: 4000000 INFO @ Mon, 29 Jun 2020 21:34:36: 14000000 INFO @ Mon, 29 Jun 2020 21:34:41: 9000000 INFO @ Mon, 29 Jun 2020 21:34:42: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:34:42: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:34:42: #1 total tags in treatment: 14982961 INFO @ Mon, 29 Jun 2020 21:34:42: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:34:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:34:42: 5000000 INFO @ Mon, 29 Jun 2020 21:34:42: #1 tags after filtering in treatment: 14982961 INFO @ Mon, 29 Jun 2020 21:34:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:34:42: #1 finished! INFO @ Mon, 29 Jun 2020 21:34:42: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:34:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:34:43: #2 number of paired peaks: 109 WARNING @ Mon, 29 Jun 2020 21:34:43: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Mon, 29 Jun 2020 21:34:43: start model_add_line... INFO @ Mon, 29 Jun 2020 21:34:44: start X-correlation... INFO @ Mon, 29 Jun 2020 21:34:44: end of X-cor INFO @ Mon, 29 Jun 2020 21:34:44: #2 finished! INFO @ Mon, 29 Jun 2020 21:34:44: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 21:34:44: #2 alternative fragment length(s) may be 1,14,47,113,167,444,522,537,585 bps INFO @ Mon, 29 Jun 2020 21:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.05_model.r WARNING @ Mon, 29 Jun 2020 21:34:44: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:34:44: #2 You may need to consider one of the other alternative d(s): 1,14,47,113,167,444,522,537,585 WARNING @ Mon, 29 Jun 2020 21:34:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:34:44: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:34:49: 10000000 INFO @ Mon, 29 Jun 2020 21:34:50: 6000000 INFO @ Mon, 29 Jun 2020 21:34:56: 11000000 INFO @ Mon, 29 Jun 2020 21:34:57: 7000000 INFO @ Mon, 29 Jun 2020 21:35:04: 12000000 INFO @ Mon, 29 Jun 2020 21:35:05: 8000000 INFO @ Mon, 29 Jun 2020 21:35:07: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:35:12: 13000000 INFO @ Mon, 29 Jun 2020 21:35:12: 9000000 INFO @ Mon, 29 Jun 2020 21:35:19: 14000000 INFO @ Mon, 29 Jun 2020 21:35:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:35:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:35:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.05_summits.bed INFO @ Mon, 29 Jun 2020 21:35:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (573 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:35:20: 10000000 INFO @ Mon, 29 Jun 2020 21:35:26: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:35:26: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:35:26: #1 total tags in treatment: 14982961 INFO @ Mon, 29 Jun 2020 21:35:26: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:35:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:35:27: #1 tags after filtering in treatment: 14982961 INFO @ Mon, 29 Jun 2020 21:35:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:35:27: #1 finished! INFO @ Mon, 29 Jun 2020 21:35:27: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:35:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:35:27: 11000000 INFO @ Mon, 29 Jun 2020 21:35:28: #2 number of paired peaks: 109 WARNING @ Mon, 29 Jun 2020 21:35:28: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Mon, 29 Jun 2020 21:35:28: start model_add_line... INFO @ Mon, 29 Jun 2020 21:35:28: start X-correlation... INFO @ Mon, 29 Jun 2020 21:35:28: end of X-cor INFO @ Mon, 29 Jun 2020 21:35:28: #2 finished! INFO @ Mon, 29 Jun 2020 21:35:28: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 21:35:28: #2 alternative fragment length(s) may be 1,14,47,113,167,444,522,537,585 bps INFO @ Mon, 29 Jun 2020 21:35:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.10_model.r WARNING @ Mon, 29 Jun 2020 21:35:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:35:28: #2 You may need to consider one of the other alternative d(s): 1,14,47,113,167,444,522,537,585 WARNING @ Mon, 29 Jun 2020 21:35:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:35:28: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:35:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:35:34: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:35:40: 13000000 INFO @ Mon, 29 Jun 2020 21:35:47: 14000000 INFO @ Mon, 29 Jun 2020 21:35:51: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:35:53: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:35:53: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:35:53: #1 total tags in treatment: 14982961 INFO @ Mon, 29 Jun 2020 21:35:53: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:35:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:35:54: #1 tags after filtering in treatment: 14982961 INFO @ Mon, 29 Jun 2020 21:35:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:35:54: #1 finished! INFO @ Mon, 29 Jun 2020 21:35:54: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:35:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:35:55: #2 number of paired peaks: 109 WARNING @ Mon, 29 Jun 2020 21:35:55: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Mon, 29 Jun 2020 21:35:55: start model_add_line... INFO @ Mon, 29 Jun 2020 21:35:55: start X-correlation... INFO @ Mon, 29 Jun 2020 21:35:55: end of X-cor INFO @ Mon, 29 Jun 2020 21:35:55: #2 finished! INFO @ Mon, 29 Jun 2020 21:35:55: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 21:35:55: #2 alternative fragment length(s) may be 1,14,47,113,167,444,522,537,585 bps INFO @ Mon, 29 Jun 2020 21:35:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.20_model.r WARNING @ Mon, 29 Jun 2020 21:35:55: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:35:55: #2 You may need to consider one of the other alternative d(s): 1,14,47,113,167,444,522,537,585 WARNING @ Mon, 29 Jun 2020 21:35:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:35:55: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:35:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:36:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:36:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:36:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.10_summits.bed INFO @ Mon, 29 Jun 2020 21:36:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (287 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:36:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 21:36:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:36:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:36:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3043410/SRX3043410.20_summits.bed INFO @ Mon, 29 Jun 2020 21:36:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (80 records, 4 fields): 1 millis CompletedMACS2peakCalling