Job ID = 6367624 SRX = SRX3583336 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:50 prefetch.2.10.7: 1) Downloading 'SRR6493992'... 2020-06-15T23:32:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:57 prefetch.2.10.7: 1) 'SRR6493992' was downloaded successfully 2020-06-15T23:41:57 prefetch.2.10.7: 'SRR6493992' has 0 unresolved dependencies Read 38739324 spots for SRR6493992/SRR6493992.sra Written 38739324 spots for SRR6493992/SRR6493992.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: 00:11:13 38739324 reads; of these: 38739324 (100.00%) were unpaired; of these: 7744292 (19.99%) aligned 0 times 26722327 (68.98%) aligned exactly 1 time 4272705 (11.03%) aligned >1 times 80.01% overall alignment rate Time searching: 00:11:13 Overall time: 00:11:13 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 16 files... [bam_rmdupse_core] 8957975 / 30995032 = 0.2890 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 09:02:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.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 09:02:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:18: 1000000 INFO @ Tue, 16 Jun 2020 09:02:23: 2000000 INFO @ Tue, 16 Jun 2020 09:02:28: 3000000 INFO @ Tue, 16 Jun 2020 09:02:33: 4000000 INFO @ Tue, 16 Jun 2020 09:02:38: 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 09:02:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.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 09:02:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:43: 6000000 INFO @ Tue, 16 Jun 2020 09:02:48: 1000000 INFO @ Tue, 16 Jun 2020 09:02:49: 7000000 INFO @ Tue, 16 Jun 2020 09:02:53: 2000000 INFO @ Tue, 16 Jun 2020 09:02:55: 8000000 INFO @ Tue, 16 Jun 2020 09:02:59: 3000000 INFO @ Tue, 16 Jun 2020 09:03:00: 9000000 INFO @ Tue, 16 Jun 2020 09:03:04: 4000000 INFO @ Tue, 16 Jun 2020 09:03:05: 10000000 INFO @ Tue, 16 Jun 2020 09:03:10: 5000000 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 09:03:11: 11000000 INFO @ Tue, 16 Jun 2020 09:03:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.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 09:03:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:03:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:03:15: 6000000 INFO @ Tue, 16 Jun 2020 09:03:16: 12000000 INFO @ Tue, 16 Jun 2020 09:03:18: 1000000 INFO @ Tue, 16 Jun 2020 09:03:21: 7000000 INFO @ Tue, 16 Jun 2020 09:03:22: 13000000 INFO @ Tue, 16 Jun 2020 09:03:23: 2000000 INFO @ Tue, 16 Jun 2020 09:03:27: 8000000 INFO @ Tue, 16 Jun 2020 09:03:28: 14000000 INFO @ Tue, 16 Jun 2020 09:03:29: 3000000 INFO @ Tue, 16 Jun 2020 09:03:32: 9000000 INFO @ Tue, 16 Jun 2020 09:03:33: 15000000 INFO @ Tue, 16 Jun 2020 09:03:34: 4000000 INFO @ Tue, 16 Jun 2020 09:03:38: 10000000 INFO @ Tue, 16 Jun 2020 09:03:39: 16000000 INFO @ Tue, 16 Jun 2020 09:03:40: 5000000 INFO @ Tue, 16 Jun 2020 09:03:43: 11000000 INFO @ Tue, 16 Jun 2020 09:03:44: 17000000 INFO @ Tue, 16 Jun 2020 09:03:45: 6000000 INFO @ Tue, 16 Jun 2020 09:03:49: 12000000 INFO @ Tue, 16 Jun 2020 09:03:50: 18000000 INFO @ Tue, 16 Jun 2020 09:03:51: 7000000 INFO @ Tue, 16 Jun 2020 09:03:54: 13000000 INFO @ Tue, 16 Jun 2020 09:03:55: 19000000 INFO @ Tue, 16 Jun 2020 09:03:57: 8000000 INFO @ Tue, 16 Jun 2020 09:04:00: 14000000 INFO @ Tue, 16 Jun 2020 09:04:01: 20000000 INFO @ Tue, 16 Jun 2020 09:04:02: 9000000 INFO @ Tue, 16 Jun 2020 09:04:06: 15000000 INFO @ Tue, 16 Jun 2020 09:04:06: 21000000 INFO @ Tue, 16 Jun 2020 09:04:07: 10000000 INFO @ Tue, 16 Jun 2020 09:04:11: 16000000 INFO @ Tue, 16 Jun 2020 09:04:12: 22000000 INFO @ Tue, 16 Jun 2020 09:04:12: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:04:12: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:04:12: #1 total tags in treatment: 22037057 INFO @ Tue, 16 Jun 2020 09:04:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:04:12: #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 09:04:13: #1 tags after filtering in treatment: 22037057 INFO @ Tue, 16 Jun 2020 09:04:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:04:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:04:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:04:13: 11000000 INFO @ Tue, 16 Jun 2020 09:04:14: #2 number of paired peaks: 123 WARNING @ Tue, 16 Jun 2020 09:04:14: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 16 Jun 2020 09:04:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:04:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:04:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:04:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:04:14: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 09:04:14: #2 alternative fragment length(s) may be 1,59,545,548,583 bps INFO @ Tue, 16 Jun 2020 09:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.05_model.r WARNING @ Tue, 16 Jun 2020 09:04:14: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:04:14: #2 You may need to consider one of the other alternative d(s): 1,59,545,548,583 WARNING @ Tue, 16 Jun 2020 09:04:14: #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 09:04:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:04:17: 17000000 INFO @ Tue, 16 Jun 2020 09:04:18: 12000000 INFO @ Tue, 16 Jun 2020 09:04:22: 18000000 INFO @ Tue, 16 Jun 2020 09:04:24: 13000000 INFO @ Tue, 16 Jun 2020 09:04:28: 19000000 INFO @ Tue, 16 Jun 2020 09:04:29: 14000000 INFO @ Tue, 16 Jun 2020 09:04:33: 20000000 INFO @ Tue, 16 Jun 2020 09:04:35: 15000000 INFO @ Tue, 16 Jun 2020 09:04:39: 21000000 INFO @ Tue, 16 Jun 2020 09:04:40: 16000000 INFO @ Tue, 16 Jun 2020 09:04:44: 22000000 INFO @ Tue, 16 Jun 2020 09:04:45: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:04:45: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:04:45: #1 total tags in treatment: 22037057 INFO @ Tue, 16 Jun 2020 09:04:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:04:45: #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 09:04:45: #1 tags after filtering in treatment: 22037057 INFO @ Tue, 16 Jun 2020 09:04:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:04:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:04:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:04:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:04:46: 17000000 INFO @ Tue, 16 Jun 2020 09:04:46: #2 number of paired peaks: 123 WARNING @ Tue, 16 Jun 2020 09:04:46: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 16 Jun 2020 09:04:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:04:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:04:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:04:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:04:46: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 09:04:46: #2 alternative fragment length(s) may be 1,59,545,548,583 bps INFO @ Tue, 16 Jun 2020 09:04:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.10_model.r WARNING @ Tue, 16 Jun 2020 09:04:46: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:04:46: #2 You may need to consider one of the other alternative d(s): 1,59,545,548,583 WARNING @ Tue, 16 Jun 2020 09:04:46: #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 09:04:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:04:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:04:51: 18000000 INFO @ Tue, 16 Jun 2020 09:04:51: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:04:57: 19000000 INFO @ Tue, 16 Jun 2020 09:05:02: 20000000 INFO @ Tue, 16 Jun 2020 09:05:08: 21000000 INFO @ Tue, 16 Jun 2020 09:05:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:05:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:05:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.05_summits.bed INFO @ Tue, 16 Jun 2020 09:05:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3385 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:05:13: 22000000 INFO @ Tue, 16 Jun 2020 09:05:14: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:05:14: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:05:14: #1 total tags in treatment: 22037057 INFO @ Tue, 16 Jun 2020 09:05:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:14: #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 09:05:14: #1 tags after filtering in treatment: 22037057 INFO @ Tue, 16 Jun 2020 09:05:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:15: #2 number of paired peaks: 123 WARNING @ Tue, 16 Jun 2020 09:05:15: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:16: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 09:05:16: #2 alternative fragment length(s) may be 1,59,545,548,583 bps INFO @ Tue, 16 Jun 2020 09:05:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.20_model.r WARNING @ Tue, 16 Jun 2020 09:05:16: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:05:16: #2 You may need to consider one of the other alternative d(s): 1,59,545,548,583 WARNING @ Tue, 16 Jun 2020 09:05:16: #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 09:05:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:05:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:05:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:05:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.10_summits.bed INFO @ Tue, 16 Jun 2020 09:05:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1832 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:05:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583336/SRX3583336.20_summits.bed INFO @ Tue, 16 Jun 2020 09:06:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (256 records, 4 fields): 3 millis CompletedMACS2peakCalling