Job ID = 6368823 SRX = SRX5985677 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:31:46 prefetch.2.10.7: 1) Downloading 'SRR9214982'... 2020-06-16T00:31:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:42:18 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:42:18 prefetch.2.10.7: 1) 'SRR9214982' was downloaded successfully Read 51680402 spots for SRR9214982/SRR9214982.sra Written 51680402 spots for SRR9214982/SRR9214982.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: 00:09:58 51680402 reads; of these: 51680402 (100.00%) were unpaired; of these: 32055065 (62.03%) aligned 0 times 16513023 (31.95%) aligned exactly 1 time 3112314 (6.02%) aligned >1 times 37.97% overall alignment rate Time searching: 00:09:58 Overall time: 00:09:58 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] 1801949 / 19625337 = 0.0918 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 10:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.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 10:02:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:40: 1000000 INFO @ Tue, 16 Jun 2020 10:02:47: 2000000 INFO @ Tue, 16 Jun 2020 10:02:53: 3000000 INFO @ Tue, 16 Jun 2020 10:03:00: 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 10:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.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 10:03:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:03:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:03:07: 5000000 INFO @ Tue, 16 Jun 2020 10:03:10: 1000000 INFO @ Tue, 16 Jun 2020 10:03:13: 6000000 INFO @ Tue, 16 Jun 2020 10:03:17: 2000000 INFO @ Tue, 16 Jun 2020 10:03:20: 7000000 INFO @ Tue, 16 Jun 2020 10:03:24: 3000000 INFO @ Tue, 16 Jun 2020 10:03:27: 8000000 INFO @ Tue, 16 Jun 2020 10:03:31: 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 10:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.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 10:03:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:03:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:03:34: 9000000 INFO @ Tue, 16 Jun 2020 10:03:38: 5000000 INFO @ Tue, 16 Jun 2020 10:03:41: 10000000 INFO @ Tue, 16 Jun 2020 10:03:41: 1000000 INFO @ Tue, 16 Jun 2020 10:03:45: 6000000 INFO @ Tue, 16 Jun 2020 10:03:48: 11000000 INFO @ Tue, 16 Jun 2020 10:03:49: 2000000 INFO @ Tue, 16 Jun 2020 10:03:52: 7000000 INFO @ Tue, 16 Jun 2020 10:03:55: 12000000 INFO @ Tue, 16 Jun 2020 10:03:56: 3000000 INFO @ Tue, 16 Jun 2020 10:03:59: 8000000 INFO @ Tue, 16 Jun 2020 10:04:02: 13000000 INFO @ Tue, 16 Jun 2020 10:04:03: 4000000 INFO @ Tue, 16 Jun 2020 10:04:07: 9000000 INFO @ Tue, 16 Jun 2020 10:04:10: 14000000 INFO @ Tue, 16 Jun 2020 10:04:10: 5000000 INFO @ Tue, 16 Jun 2020 10:04:14: 10000000 INFO @ Tue, 16 Jun 2020 10:04:17: 15000000 INFO @ Tue, 16 Jun 2020 10:04:17: 6000000 INFO @ Tue, 16 Jun 2020 10:04:21: 11000000 INFO @ Tue, 16 Jun 2020 10:04:24: 16000000 INFO @ Tue, 16 Jun 2020 10:04:24: 7000000 INFO @ Tue, 16 Jun 2020 10:04:28: 12000000 INFO @ Tue, 16 Jun 2020 10:04:32: 17000000 INFO @ Tue, 16 Jun 2020 10:04:32: 8000000 INFO @ Tue, 16 Jun 2020 10:04:35: 13000000 INFO @ Tue, 16 Jun 2020 10:04:37: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:04:37: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:04:37: #1 total tags in treatment: 17823388 INFO @ Tue, 16 Jun 2020 10:04:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:04:37: #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 10:04:38: #1 tags after filtering in treatment: 17823388 INFO @ Tue, 16 Jun 2020 10:04:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:04:38: #1 finished! INFO @ Tue, 16 Jun 2020 10:04:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:04:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:04:39: 9000000 INFO @ Tue, 16 Jun 2020 10:04:39: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 10:04:39: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 10:04:39: start model_add_line... INFO @ Tue, 16 Jun 2020 10:04:39: start X-correlation... INFO @ Tue, 16 Jun 2020 10:04:39: end of X-cor INFO @ Tue, 16 Jun 2020 10:04:39: #2 finished! INFO @ Tue, 16 Jun 2020 10:04:39: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 10:04:39: #2 alternative fragment length(s) may be 2,72 bps INFO @ Tue, 16 Jun 2020 10:04:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.05_model.r WARNING @ Tue, 16 Jun 2020 10:04:39: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:04:39: #2 You may need to consider one of the other alternative d(s): 2,72 WARNING @ Tue, 16 Jun 2020 10:04:39: #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 10:04:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:04:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:04:42: 14000000 INFO @ Tue, 16 Jun 2020 10:04:45: 10000000 INFO @ Tue, 16 Jun 2020 10:04:50: 15000000 INFO @ Tue, 16 Jun 2020 10:04:52: 11000000 INFO @ Tue, 16 Jun 2020 10:04:57: 16000000 INFO @ Tue, 16 Jun 2020 10:04:59: 12000000 INFO @ Tue, 16 Jun 2020 10:05:04: 17000000 INFO @ Tue, 16 Jun 2020 10:05:06: 13000000 INFO @ Tue, 16 Jun 2020 10:05:10: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:05:10: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:05:10: #1 total tags in treatment: 17823388 INFO @ Tue, 16 Jun 2020 10:05:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:05:10: #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 10:05:10: #1 tags after filtering in treatment: 17823388 INFO @ Tue, 16 Jun 2020 10:05:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:05:10: #1 finished! INFO @ Tue, 16 Jun 2020 10:05:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:05:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:05:11: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 10:05:11: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 10:05:11: start model_add_line... INFO @ Tue, 16 Jun 2020 10:05:11: start X-correlation... INFO @ Tue, 16 Jun 2020 10:05:11: end of X-cor INFO @ Tue, 16 Jun 2020 10:05:11: #2 finished! INFO @ Tue, 16 Jun 2020 10:05:11: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 10:05:11: #2 alternative fragment length(s) may be 2,72 bps INFO @ Tue, 16 Jun 2020 10:05:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.10_model.r WARNING @ Tue, 16 Jun 2020 10:05:11: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:05:11: #2 You may need to consider one of the other alternative d(s): 2,72 WARNING @ Tue, 16 Jun 2020 10:05:11: #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 10:05:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:05:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:05:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:05:13: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:05:20: 15000000 INFO @ Tue, 16 Jun 2020 10:05:27: 16000000 INFO @ Tue, 16 Jun 2020 10:05:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:05:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:05:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.05_summits.bed INFO @ Tue, 16 Jun 2020 10:05:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:05:33: 17000000 INFO @ Tue, 16 Jun 2020 10:05:39: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:05:39: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:05:39: #1 total tags in treatment: 17823388 INFO @ Tue, 16 Jun 2020 10:05:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:05:39: #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 10:05:39: #1 tags after filtering in treatment: 17823388 INFO @ Tue, 16 Jun 2020 10:05:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:05:39: #1 finished! INFO @ Tue, 16 Jun 2020 10:05:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:05:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:05:40: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 10:05:40: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 10:05:40: start model_add_line... INFO @ Tue, 16 Jun 2020 10:05:40: start X-correlation... INFO @ Tue, 16 Jun 2020 10:05:40: end of X-cor INFO @ Tue, 16 Jun 2020 10:05:40: #2 finished! INFO @ Tue, 16 Jun 2020 10:05:40: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 10:05:40: #2 alternative fragment length(s) may be 2,72 bps INFO @ Tue, 16 Jun 2020 10:05:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.20_model.r WARNING @ Tue, 16 Jun 2020 10:05:40: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:05:40: #2 You may need to consider one of the other alternative d(s): 2,72 WARNING @ Tue, 16 Jun 2020 10:05:40: #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 10:05:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:05:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:05:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.10_summits.bed INFO @ Tue, 16 Jun 2020 10:05:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:06:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:06:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:06:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:06:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985677/SRX5985677.20_summits.bed INFO @ Tue, 16 Jun 2020 10:06:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 2 millis CompletedMACS2peakCalling