Job ID = 6368357 SRX = SRX495037 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:13:06 prefetch.2.10.7: 1) Downloading 'SRR1198569'... 2020-06-16T00:13:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:15:58 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:15:58 prefetch.2.10.7: 1) 'SRR1198569' was downloaded successfully Read 22970231 spots for SRR1198569/SRR1198569.sra Written 22970231 spots for SRR1198569/SRR1198569.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: 00:05:11 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517103 (10.96%) aligned 0 times 16806077 (73.16%) aligned exactly 1 time 3647051 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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] 2296858 / 20453128 = 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 09:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.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 09:27:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:58: 1000000 INFO @ Tue, 16 Jun 2020 09:28:04: 2000000 INFO @ Tue, 16 Jun 2020 09:28:09: 3000000 INFO @ Tue, 16 Jun 2020 09:28:15: 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 09:28:21: 5000000 INFO @ Tue, 16 Jun 2020 09:28:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.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 09:28:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:28: 6000000 INFO @ Tue, 16 Jun 2020 09:28:28: 1000000 INFO @ Tue, 16 Jun 2020 09:28:34: 7000000 INFO @ Tue, 16 Jun 2020 09:28:34: 2000000 INFO @ Tue, 16 Jun 2020 09:28:39: 8000000 INFO @ Tue, 16 Jun 2020 09:28:39: 3000000 INFO @ Tue, 16 Jun 2020 09:28:45: 9000000 INFO @ Tue, 16 Jun 2020 09:28:45: 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 09:28:51: 10000000 INFO @ Tue, 16 Jun 2020 09:28:51: 5000000 INFO @ Tue, 16 Jun 2020 09:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.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 09:28:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:57: 11000000 INFO @ Tue, 16 Jun 2020 09:28:57: 6000000 INFO @ Tue, 16 Jun 2020 09:28:58: 1000000 INFO @ Tue, 16 Jun 2020 09:29:03: 7000000 INFO @ Tue, 16 Jun 2020 09:29:03: 12000000 INFO @ Tue, 16 Jun 2020 09:29:04: 2000000 INFO @ Tue, 16 Jun 2020 09:29:09: 8000000 INFO @ Tue, 16 Jun 2020 09:29:09: 13000000 INFO @ Tue, 16 Jun 2020 09:29:10: 3000000 INFO @ Tue, 16 Jun 2020 09:29:15: 9000000 INFO @ Tue, 16 Jun 2020 09:29:15: 14000000 INFO @ Tue, 16 Jun 2020 09:29:16: 4000000 INFO @ Tue, 16 Jun 2020 09:29:20: 10000000 INFO @ Tue, 16 Jun 2020 09:29:21: 15000000 INFO @ Tue, 16 Jun 2020 09:29:23: 5000000 INFO @ Tue, 16 Jun 2020 09:29:26: 11000000 INFO @ Tue, 16 Jun 2020 09:29:28: 16000000 INFO @ Tue, 16 Jun 2020 09:29:29: 6000000 INFO @ Tue, 16 Jun 2020 09:29:32: 12000000 INFO @ Tue, 16 Jun 2020 09:29:34: 17000000 INFO @ Tue, 16 Jun 2020 09:29:35: 7000000 INFO @ Tue, 16 Jun 2020 09:29:38: 13000000 INFO @ Tue, 16 Jun 2020 09:29:40: 18000000 INFO @ Tue, 16 Jun 2020 09:29:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:29:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:29:41: #1 total tags in treatment: 18156270 INFO @ Tue, 16 Jun 2020 09:29:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:41: #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 09:29:41: 8000000 INFO @ Tue, 16 Jun 2020 09:29:41: #1 tags after filtering in treatment: 18156270 INFO @ Tue, 16 Jun 2020 09:29:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:42: #2 number of paired peaks: 265 WARNING @ Tue, 16 Jun 2020 09:29:42: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:43: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:29:43: #2 alternative fragment length(s) may be 1,39,564,567 bps INFO @ Tue, 16 Jun 2020 09:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.05_model.r WARNING @ Tue, 16 Jun 2020 09:29:43: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:43: #2 You may need to consider one of the other alternative d(s): 1,39,564,567 WARNING @ Tue, 16 Jun 2020 09:29:43: #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 09:29:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:44: 14000000 INFO @ Tue, 16 Jun 2020 09:29:47: 9000000 INFO @ Tue, 16 Jun 2020 09:29:50: 15000000 INFO @ Tue, 16 Jun 2020 09:29:53: 10000000 INFO @ Tue, 16 Jun 2020 09:29:56: 16000000 INFO @ Tue, 16 Jun 2020 09:29:59: 11000000 INFO @ Tue, 16 Jun 2020 09:30:02: 17000000 INFO @ Tue, 16 Jun 2020 09:30:05: 12000000 INFO @ Tue, 16 Jun 2020 09:30:08: 18000000 INFO @ Tue, 16 Jun 2020 09:30:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:30:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:30:09: #1 total tags in treatment: 18156270 INFO @ Tue, 16 Jun 2020 09:30:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:09: #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 09:30:09: #1 tags after filtering in treatment: 18156270 INFO @ Tue, 16 Jun 2020 09:30:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:10: #2 number of paired peaks: 265 WARNING @ Tue, 16 Jun 2020 09:30:10: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:11: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:30:11: #2 alternative fragment length(s) may be 1,39,564,567 bps INFO @ Tue, 16 Jun 2020 09:30:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.10_model.r WARNING @ Tue, 16 Jun 2020 09:30:11: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:11: #2 You may need to consider one of the other alternative d(s): 1,39,564,567 WARNING @ Tue, 16 Jun 2020 09:30:11: #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 09:30:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:11: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:30:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:17: 14000000 INFO @ Tue, 16 Jun 2020 09:30:23: 15000000 INFO @ Tue, 16 Jun 2020 09:30:29: 16000000 INFO @ Tue, 16 Jun 2020 09:30:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.05_summits.bed INFO @ Tue, 16 Jun 2020 09:30:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (783 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:34: 17000000 INFO @ Tue, 16 Jun 2020 09:30:40: 18000000 INFO @ Tue, 16 Jun 2020 09:30:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:30:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:30:41: #1 total tags in treatment: 18156270 INFO @ Tue, 16 Jun 2020 09:30:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:41: #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 09:30:42: #1 tags after filtering in treatment: 18156270 INFO @ Tue, 16 Jun 2020 09:30:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:43: #2 number of paired peaks: 265 WARNING @ Tue, 16 Jun 2020 09:30:43: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:43: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:30:43: #2 alternative fragment length(s) may be 1,39,564,567 bps INFO @ Tue, 16 Jun 2020 09:30:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.20_model.r WARNING @ Tue, 16 Jun 2020 09:30:43: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:43: #2 You may need to consider one of the other alternative d(s): 1,39,564,567 WARNING @ Tue, 16 Jun 2020 09:30:43: #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 09:30:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.10_summits.bed INFO @ Tue, 16 Jun 2020 09:30:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (438 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495037/SRX495037.20_summits.bed INFO @ Tue, 16 Jun 2020 09:31:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (154 records, 4 fields): 1 millis CompletedMACS2peakCalling