Job ID = 6368411 SRX = SRX495090 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:15:36 prefetch.2.10.7: 1) Downloading 'SRR1198622'... 2020-06-16T00:15:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:18:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:18:18 prefetch.2.10.7: 'SRR1198622' is valid 2020-06-16T00:18:18 prefetch.2.10.7: 1) 'SRR1198622' was downloaded successfully Read 18854814 spots for SRR1198622/SRR1198622.sra Written 18854814 spots for SRR1198622/SRR1198622.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: 00:03:22 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 288213 (1.53%) aligned 0 times 14954443 (79.31%) aligned exactly 1 time 3612158 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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] 3522414 / 18566601 = 0.1897 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 09:27:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.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 09:27:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:42: 1000000 INFO @ Tue, 16 Jun 2020 09:27:47: 2000000 INFO @ Tue, 16 Jun 2020 09:27:52: 3000000 INFO @ Tue, 16 Jun 2020 09:27:56: 4000000 INFO @ Tue, 16 Jun 2020 09:28:01: 5000000 INFO @ Tue, 16 Jun 2020 09:28:05: 6000000 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 09:28:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.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 09:28:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:10: 7000000 INFO @ Tue, 16 Jun 2020 09:28:13: 1000000 INFO @ Tue, 16 Jun 2020 09:28:15: 8000000 INFO @ Tue, 16 Jun 2020 09:28:18: 2000000 INFO @ Tue, 16 Jun 2020 09:28:20: 9000000 INFO @ Tue, 16 Jun 2020 09:28:24: 3000000 INFO @ Tue, 16 Jun 2020 09:28:25: 10000000 INFO @ Tue, 16 Jun 2020 09:28:28: 4000000 INFO @ Tue, 16 Jun 2020 09:28:30: 11000000 INFO @ Tue, 16 Jun 2020 09:28:34: 5000000 INFO @ Tue, 16 Jun 2020 09:28:35: 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 09:28:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.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 09:28:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:39: 6000000 INFO @ Tue, 16 Jun 2020 09:28:40: 13000000 INFO @ Tue, 16 Jun 2020 09:28:43: 1000000 INFO @ Tue, 16 Jun 2020 09:28:44: 7000000 INFO @ Tue, 16 Jun 2020 09:28:45: 14000000 INFO @ Tue, 16 Jun 2020 09:28:47: 2000000 INFO @ Tue, 16 Jun 2020 09:28:49: 8000000 INFO @ Tue, 16 Jun 2020 09:28:50: 15000000 INFO @ Tue, 16 Jun 2020 09:28:51: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:28:51: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:28:51: #1 total tags in treatment: 15044187 INFO @ Tue, 16 Jun 2020 09:28:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:51: #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 09:28:51: #1 tags after filtering in treatment: 15044187 INFO @ Tue, 16 Jun 2020 09:28:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:52: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 09:28:52: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:52: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:28:52: #2 alternative fragment length(s) may be 2,45,590 bps INFO @ Tue, 16 Jun 2020 09:28:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.05_model.r WARNING @ Tue, 16 Jun 2020 09:28:52: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:52: #2 You may need to consider one of the other alternative d(s): 2,45,590 WARNING @ Tue, 16 Jun 2020 09:28:52: #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 09:28:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:52: 3000000 INFO @ Tue, 16 Jun 2020 09:28:54: 9000000 INFO @ Tue, 16 Jun 2020 09:28:57: 4000000 INFO @ Tue, 16 Jun 2020 09:28:58: 10000000 INFO @ Tue, 16 Jun 2020 09:29:01: 5000000 INFO @ Tue, 16 Jun 2020 09:29:03: 11000000 INFO @ Tue, 16 Jun 2020 09:29:06: 6000000 INFO @ Tue, 16 Jun 2020 09:29:08: 12000000 INFO @ Tue, 16 Jun 2020 09:29:11: 7000000 INFO @ Tue, 16 Jun 2020 09:29:12: 13000000 INFO @ Tue, 16 Jun 2020 09:29:16: 8000000 INFO @ Tue, 16 Jun 2020 09:29:17: 14000000 INFO @ Tue, 16 Jun 2020 09:29:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:20: 9000000 INFO @ Tue, 16 Jun 2020 09:29:21: 15000000 INFO @ Tue, 16 Jun 2020 09:29:21: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:29:21: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:29:21: #1 total tags in treatment: 15044187 INFO @ Tue, 16 Jun 2020 09:29:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:21: #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 09:29:22: #1 tags after filtering in treatment: 15044187 INFO @ Tue, 16 Jun 2020 09:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:23: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 09:29:23: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:23: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:29:23: #2 alternative fragment length(s) may be 2,45,590 bps INFO @ Tue, 16 Jun 2020 09:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.10_model.r WARNING @ Tue, 16 Jun 2020 09:29:23: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:23: #2 You may need to consider one of the other alternative d(s): 2,45,590 WARNING @ Tue, 16 Jun 2020 09:29:23: #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 09:29:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:25: 10000000 INFO @ Tue, 16 Jun 2020 09:29:30: 11000000 INFO @ Tue, 16 Jun 2020 09:29:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3850 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:34: 12000000 INFO @ Tue, 16 Jun 2020 09:29:39: 13000000 INFO @ Tue, 16 Jun 2020 09:29:43: 14000000 INFO @ Tue, 16 Jun 2020 09:29:48: 15000000 INFO @ Tue, 16 Jun 2020 09:29:48: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:29:48: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:29:48: #1 total tags in treatment: 15044187 INFO @ Tue, 16 Jun 2020 09:29:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:48: #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 09:29:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:48: #1 tags after filtering in treatment: 15044187 INFO @ Tue, 16 Jun 2020 09:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:49: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 09:29:49: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:50: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:29:50: #2 alternative fragment length(s) may be 2,45,590 bps INFO @ Tue, 16 Jun 2020 09:29:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.20_model.r WARNING @ Tue, 16 Jun 2020 09:29:50: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:50: #2 You may need to consider one of the other alternative d(s): 2,45,590 WARNING @ Tue, 16 Jun 2020 09:29:50: #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 09:29:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:30:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.10_summits.bed INFO @ Tue, 16 Jun 2020 09:30:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (934 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495090/SRX495090.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (267 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。