Job ID = 6368361 SRX = SRX495041 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:18:36 prefetch.2.10.7: 1) Downloading 'SRR1198573'... 2020-06-16T00:18:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:21:36 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:21:36 prefetch.2.10.7: 1) 'SRR1198573' was downloaded successfully Read 22970231 spots for SRR1198573/SRR1198573.sra Written 22970231 spots for SRR1198573/SRR1198573.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: 00:05:03 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517140 (10.96%) aligned 0 times 16806182 (73.17%) aligned exactly 1 time 3646909 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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] 2297498 / 20453091 = 0.1123 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 09:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.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 09:33:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:15: 1000000 INFO @ Tue, 16 Jun 2020 09:33:19: 2000000 INFO @ Tue, 16 Jun 2020 09:33:24: 3000000 INFO @ Tue, 16 Jun 2020 09:33:29: 4000000 INFO @ Tue, 16 Jun 2020 09:33:34: 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 09:33:38: 6000000 INFO @ Tue, 16 Jun 2020 09:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.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 09:33:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:43: 7000000 INFO @ Tue, 16 Jun 2020 09:33:45: 1000000 INFO @ Tue, 16 Jun 2020 09:33:48: 8000000 INFO @ Tue, 16 Jun 2020 09:33:50: 2000000 INFO @ Tue, 16 Jun 2020 09:33:53: 9000000 INFO @ Tue, 16 Jun 2020 09:33:55: 3000000 INFO @ Tue, 16 Jun 2020 09:33:58: 10000000 INFO @ Tue, 16 Jun 2020 09:34:00: 4000000 INFO @ Tue, 16 Jun 2020 09:34:03: 11000000 INFO @ Tue, 16 Jun 2020 09:34:04: 5000000 INFO @ Tue, 16 Jun 2020 09:34:08: 12000000 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 09:34:09: 6000000 INFO @ Tue, 16 Jun 2020 09:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.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 09:34:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:13: 13000000 INFO @ Tue, 16 Jun 2020 09:34:14: 7000000 INFO @ Tue, 16 Jun 2020 09:34:15: 1000000 INFO @ Tue, 16 Jun 2020 09:34:18: 14000000 INFO @ Tue, 16 Jun 2020 09:34:19: 8000000 INFO @ Tue, 16 Jun 2020 09:34:20: 2000000 INFO @ Tue, 16 Jun 2020 09:34:23: 15000000 INFO @ Tue, 16 Jun 2020 09:34:24: 9000000 INFO @ Tue, 16 Jun 2020 09:34:25: 3000000 INFO @ Tue, 16 Jun 2020 09:34:28: 16000000 INFO @ Tue, 16 Jun 2020 09:34:29: 10000000 INFO @ Tue, 16 Jun 2020 09:34:30: 4000000 INFO @ Tue, 16 Jun 2020 09:34:33: 17000000 INFO @ Tue, 16 Jun 2020 09:34:34: 11000000 INFO @ Tue, 16 Jun 2020 09:34:35: 5000000 INFO @ Tue, 16 Jun 2020 09:34:38: 18000000 INFO @ Tue, 16 Jun 2020 09:34:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:34:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:34:39: #1 total tags in treatment: 18155593 INFO @ Tue, 16 Jun 2020 09:34:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:39: #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 09:34:39: 12000000 INFO @ Tue, 16 Jun 2020 09:34:40: #1 tags after filtering in treatment: 18155593 INFO @ Tue, 16 Jun 2020 09:34:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:40: 6000000 INFO @ Tue, 16 Jun 2020 09:34:41: #2 number of paired peaks: 258 WARNING @ Tue, 16 Jun 2020 09:34:41: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:41: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:34:41: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:34:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.05_model.r WARNING @ Tue, 16 Jun 2020 09:34:41: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:41: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:34:41: #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 09:34:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:44: 13000000 INFO @ Tue, 16 Jun 2020 09:34:45: 7000000 INFO @ Tue, 16 Jun 2020 09:34:49: 14000000 INFO @ Tue, 16 Jun 2020 09:34:50: 8000000 INFO @ Tue, 16 Jun 2020 09:34:54: 15000000 INFO @ Tue, 16 Jun 2020 09:34:55: 9000000 INFO @ Tue, 16 Jun 2020 09:34:59: 16000000 INFO @ Tue, 16 Jun 2020 09:35:00: 10000000 INFO @ Tue, 16 Jun 2020 09:35:04: 17000000 INFO @ Tue, 16 Jun 2020 09:35:05: 11000000 INFO @ Tue, 16 Jun 2020 09:35:09: 18000000 INFO @ Tue, 16 Jun 2020 09:35:10: 12000000 INFO @ Tue, 16 Jun 2020 09:35:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:35:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:35:10: #1 total tags in treatment: 18155593 INFO @ Tue, 16 Jun 2020 09:35:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:10: #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 09:35:10: #1 tags after filtering in treatment: 18155593 INFO @ Tue, 16 Jun 2020 09:35:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:12: #2 number of paired peaks: 258 WARNING @ Tue, 16 Jun 2020 09:35:12: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:12: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:35:12: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:35:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.10_model.r WARNING @ Tue, 16 Jun 2020 09:35:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:12: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:35:12: #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 09:35:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:15: 13000000 INFO @ Tue, 16 Jun 2020 09:35:20: 14000000 INFO @ Tue, 16 Jun 2020 09:35:25: 15000000 INFO @ Tue, 16 Jun 2020 09:35:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (781 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:30: 16000000 INFO @ Tue, 16 Jun 2020 09:35:34: 17000000 INFO @ Tue, 16 Jun 2020 09:35:39: 18000000 INFO @ Tue, 16 Jun 2020 09:35:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:35:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:35:40: #1 total tags in treatment: 18155593 INFO @ Tue, 16 Jun 2020 09:35:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:40: #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 09:35:40: #1 tags after filtering in treatment: 18155593 INFO @ Tue, 16 Jun 2020 09:35:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:40: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:41: #2 number of paired peaks: 258 WARNING @ Tue, 16 Jun 2020 09:35:41: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:42: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:35:42: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:35:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.20_model.r WARNING @ Tue, 16 Jun 2020 09:35:42: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:42: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:35:42: #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 09:35:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (470 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:36:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495041/SRX495041.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (182 records, 4 fields): 2 millis CompletedMACS2peakCalling