Job ID = 6368495 SRX = SRX5020725 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:17:25 prefetch.2.10.7: 1) Downloading 'SRR8201348'... 2020-06-16T00:17:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:21:22 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:21:22 prefetch.2.10.7: 1) 'SRR8201348' was downloaded successfully Read 18323763 spots for SRR8201348/SRR8201348.sra Written 18323763 spots for SRR8201348/SRR8201348.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: 00:04:28 18323763 reads; of these: 18323763 (100.00%) were unpaired; of these: 325916 (1.78%) aligned 0 times 14635019 (79.87%) aligned exactly 1 time 3362828 (18.35%) aligned >1 times 98.22% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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] 2154824 / 17997847 = 0.1197 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 09:32:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.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 09:32:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:07: 1000000 INFO @ Tue, 16 Jun 2020 09:32:14: 2000000 INFO @ Tue, 16 Jun 2020 09:32:21: 3000000 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 09:32:27: 4000000 INFO @ Tue, 16 Jun 2020 09:32:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.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 09:32:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:34: 5000000 INFO @ Tue, 16 Jun 2020 09:32:36: 1000000 INFO @ Tue, 16 Jun 2020 09:32:41: 6000000 INFO @ Tue, 16 Jun 2020 09:32:44: 2000000 INFO @ Tue, 16 Jun 2020 09:32:49: 7000000 INFO @ Tue, 16 Jun 2020 09:32:51: 3000000 INFO @ Tue, 16 Jun 2020 09:32:56: 8000000 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 09:32:58: 4000000 INFO @ Tue, 16 Jun 2020 09:32:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.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 09:32:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:03: 9000000 INFO @ Tue, 16 Jun 2020 09:33:06: 5000000 INFO @ Tue, 16 Jun 2020 09:33:06: 1000000 INFO @ Tue, 16 Jun 2020 09:33:10: 10000000 INFO @ Tue, 16 Jun 2020 09:33:13: 6000000 INFO @ Tue, 16 Jun 2020 09:33:13: 2000000 INFO @ Tue, 16 Jun 2020 09:33:17: 11000000 INFO @ Tue, 16 Jun 2020 09:33:21: 7000000 INFO @ Tue, 16 Jun 2020 09:33:21: 3000000 INFO @ Tue, 16 Jun 2020 09:33:24: 12000000 INFO @ Tue, 16 Jun 2020 09:33:28: 8000000 INFO @ Tue, 16 Jun 2020 09:33:28: 4000000 INFO @ Tue, 16 Jun 2020 09:33:31: 13000000 INFO @ Tue, 16 Jun 2020 09:33:35: 9000000 INFO @ Tue, 16 Jun 2020 09:33:35: 5000000 INFO @ Tue, 16 Jun 2020 09:33:38: 14000000 INFO @ Tue, 16 Jun 2020 09:33:42: 10000000 INFO @ Tue, 16 Jun 2020 09:33:42: 6000000 INFO @ Tue, 16 Jun 2020 09:33:45: 15000000 INFO @ Tue, 16 Jun 2020 09:33:49: 11000000 INFO @ Tue, 16 Jun 2020 09:33:49: 7000000 INFO @ Tue, 16 Jun 2020 09:33:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:51: #1 total tags in treatment: 15843023 INFO @ Tue, 16 Jun 2020 09:33:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:51: #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 09:33:51: #1 tags after filtering in treatment: 15843023 INFO @ Tue, 16 Jun 2020 09:33:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:52: #2 number of paired peaks: 259 WARNING @ Tue, 16 Jun 2020 09:33:52: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:52: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:33:52: #2 alternative fragment length(s) may be 2,52,559,590 bps INFO @ Tue, 16 Jun 2020 09:33:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.05_model.r WARNING @ Tue, 16 Jun 2020 09:33:52: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:52: #2 You may need to consider one of the other alternative d(s): 2,52,559,590 WARNING @ Tue, 16 Jun 2020 09:33:52: #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 09:33:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:56: 12000000 INFO @ Tue, 16 Jun 2020 09:33:56: 8000000 INFO @ Tue, 16 Jun 2020 09:34:03: 13000000 INFO @ Tue, 16 Jun 2020 09:34:03: 9000000 INFO @ Tue, 16 Jun 2020 09:34:10: 14000000 INFO @ Tue, 16 Jun 2020 09:34:10: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:34:17: 15000000 INFO @ Tue, 16 Jun 2020 09:34:17: 11000000 INFO @ Tue, 16 Jun 2020 09:34:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:23: #1 total tags in treatment: 15843023 INFO @ Tue, 16 Jun 2020 09:34:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:23: #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 09:34:23: #1 tags after filtering in treatment: 15843023 INFO @ Tue, 16 Jun 2020 09:34:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:24: 12000000 INFO @ Tue, 16 Jun 2020 09:34:25: #2 number of paired peaks: 259 WARNING @ Tue, 16 Jun 2020 09:34:25: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:25: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:34:25: #2 alternative fragment length(s) may be 2,52,559,590 bps INFO @ Tue, 16 Jun 2020 09:34:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.10_model.r WARNING @ Tue, 16 Jun 2020 09:34:25: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:25: #2 You may need to consider one of the other alternative d(s): 2,52,559,590 WARNING @ Tue, 16 Jun 2020 09:34:25: #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 09:34:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:30: 13000000 INFO @ Tue, 16 Jun 2020 09:34:37: 14000000 INFO @ Tue, 16 Jun 2020 09:34:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.05_summits.bed INFO @ Tue, 16 Jun 2020 09:34:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1287 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:43: 15000000 INFO @ Tue, 16 Jun 2020 09:34:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:49: #1 total tags in treatment: 15843023 INFO @ Tue, 16 Jun 2020 09:34:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:49: #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 09:34:49: #1 tags after filtering in treatment: 15843023 INFO @ Tue, 16 Jun 2020 09:34:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:50: #2 number of paired peaks: 259 WARNING @ Tue, 16 Jun 2020 09:34:50: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:50: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:34:50: #2 alternative fragment length(s) may be 2,52,559,590 bps INFO @ Tue, 16 Jun 2020 09:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.20_model.r WARNING @ Tue, 16 Jun 2020 09:34:50: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:50: #2 You may need to consider one of the other alternative d(s): 2,52,559,590 WARNING @ Tue, 16 Jun 2020 09:34:50: #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 09:34:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (469 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020725/SRX5020725.20_summits.bed INFO @ Tue, 16 Jun 2020 09:35:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 1 millis CompletedMACS2peakCalling