Job ID = 6366266 SRX = SRX1007138 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:43:52 prefetch.2.10.7: 1) Downloading 'SRR1993098'... 2020-06-15T22:43:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:21 prefetch.2.10.7: 1) 'SRR1993098' was downloaded successfully Read 38254702 spots for SRR1993098/SRR1993098.sra Written 38254702 spots for SRR1993098/SRR1993098.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: 00:06:01 38254702 reads; of these: 38254702 (100.00%) were unpaired; of these: 8894882 (23.25%) aligned 0 times 25017028 (65.40%) aligned exactly 1 time 4342792 (11.35%) aligned >1 times 76.75% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 6864220 / 29359820 = 0.2338 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 08:01:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.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 08:01:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:54: 1000000 INFO @ Tue, 16 Jun 2020 08:02:00: 2000000 INFO @ Tue, 16 Jun 2020 08:02:07: 3000000 INFO @ Tue, 16 Jun 2020 08:02:14: 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 08:02:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.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 08:02:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:21: 5000000 INFO @ Tue, 16 Jun 2020 08:02:24: 1000000 INFO @ Tue, 16 Jun 2020 08:02:29: 6000000 INFO @ Tue, 16 Jun 2020 08:02:32: 2000000 INFO @ Tue, 16 Jun 2020 08:02:36: 7000000 INFO @ Tue, 16 Jun 2020 08:02:39: 3000000 INFO @ Tue, 16 Jun 2020 08:02:44: 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 08:02:46: 4000000 INFO @ Tue, 16 Jun 2020 08:02:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.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 08:02:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:51: 9000000 INFO @ Tue, 16 Jun 2020 08:02:54: 5000000 INFO @ Tue, 16 Jun 2020 08:02:54: 1000000 INFO @ Tue, 16 Jun 2020 08:02:59: 10000000 INFO @ Tue, 16 Jun 2020 08:03:01: 2000000 INFO @ Tue, 16 Jun 2020 08:03:02: 6000000 INFO @ Tue, 16 Jun 2020 08:03:07: 11000000 INFO @ Tue, 16 Jun 2020 08:03:09: 3000000 INFO @ Tue, 16 Jun 2020 08:03:10: 7000000 INFO @ Tue, 16 Jun 2020 08:03:15: 12000000 INFO @ Tue, 16 Jun 2020 08:03:16: 4000000 INFO @ Tue, 16 Jun 2020 08:03:18: 8000000 INFO @ Tue, 16 Jun 2020 08:03:23: 13000000 INFO @ Tue, 16 Jun 2020 08:03:23: 5000000 INFO @ Tue, 16 Jun 2020 08:03:26: 9000000 INFO @ Tue, 16 Jun 2020 08:03:31: 6000000 INFO @ Tue, 16 Jun 2020 08:03:31: 14000000 INFO @ Tue, 16 Jun 2020 08:03:34: 10000000 INFO @ Tue, 16 Jun 2020 08:03:38: 7000000 INFO @ Tue, 16 Jun 2020 08:03:39: 15000000 INFO @ Tue, 16 Jun 2020 08:03:42: 11000000 INFO @ Tue, 16 Jun 2020 08:03:45: 8000000 INFO @ Tue, 16 Jun 2020 08:03:47: 16000000 INFO @ Tue, 16 Jun 2020 08:03:50: 12000000 INFO @ Tue, 16 Jun 2020 08:03:53: 9000000 INFO @ Tue, 16 Jun 2020 08:03:55: 17000000 INFO @ Tue, 16 Jun 2020 08:03:58: 13000000 INFO @ Tue, 16 Jun 2020 08:04:00: 10000000 INFO @ Tue, 16 Jun 2020 08:04:03: 18000000 INFO @ Tue, 16 Jun 2020 08:04:06: 14000000 INFO @ Tue, 16 Jun 2020 08:04:08: 11000000 INFO @ Tue, 16 Jun 2020 08:04:11: 19000000 INFO @ Tue, 16 Jun 2020 08:04:14: 15000000 INFO @ Tue, 16 Jun 2020 08:04:15: 12000000 INFO @ Tue, 16 Jun 2020 08:04:19: 20000000 INFO @ Tue, 16 Jun 2020 08:04:22: 16000000 INFO @ Tue, 16 Jun 2020 08:04:23: 13000000 INFO @ Tue, 16 Jun 2020 08:04:27: 21000000 INFO @ Tue, 16 Jun 2020 08:04:30: 17000000 INFO @ Tue, 16 Jun 2020 08:04:30: 14000000 INFO @ Tue, 16 Jun 2020 08:04:35: 22000000 INFO @ Tue, 16 Jun 2020 08:04:38: 15000000 INFO @ Tue, 16 Jun 2020 08:04:38: 18000000 INFO @ Tue, 16 Jun 2020 08:04:39: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:04:39: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:04:39: #1 total tags in treatment: 22495600 INFO @ Tue, 16 Jun 2020 08:04:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:39: #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 08:04:39: #1 tags after filtering in treatment: 22495600 INFO @ Tue, 16 Jun 2020 08:04:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:39: #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 08:04:41: #2 number of paired peaks: 579 WARNING @ Tue, 16 Jun 2020 08:04:41: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:41: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:04:41: #2 alternative fragment length(s) may be 3,57 bps INFO @ Tue, 16 Jun 2020 08:04:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.05_model.r WARNING @ Tue, 16 Jun 2020 08:04:41: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:41: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Tue, 16 Jun 2020 08:04:41: #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 08:04:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:45: 16000000 INFO @ Tue, 16 Jun 2020 08:04:46: 19000000 INFO @ Tue, 16 Jun 2020 08:04:52: 17000000 INFO @ Tue, 16 Jun 2020 08:04:55: 20000000 INFO @ Tue, 16 Jun 2020 08:05:00: 18000000 INFO @ Tue, 16 Jun 2020 08:05:03: 21000000 INFO @ Tue, 16 Jun 2020 08:05:08: 19000000 INFO @ Tue, 16 Jun 2020 08:05:11: 22000000 INFO @ Tue, 16 Jun 2020 08:05:15: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:05:15: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:05:15: #1 total tags in treatment: 22495600 INFO @ Tue, 16 Jun 2020 08:05:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:15: #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 08:05:16: #1 tags after filtering in treatment: 22495600 INFO @ Tue, 16 Jun 2020 08:05:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:16: 20000000 INFO @ Tue, 16 Jun 2020 08:05:18: #2 number of paired peaks: 579 WARNING @ Tue, 16 Jun 2020 08:05:18: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:18: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:05:18: #2 alternative fragment length(s) may be 3,57 bps INFO @ Tue, 16 Jun 2020 08:05:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.10_model.r WARNING @ Tue, 16 Jun 2020 08:05:18: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:18: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Tue, 16 Jun 2020 08:05:18: #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 08:05:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:22: 21000000 INFO @ Tue, 16 Jun 2020 08:05:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:05:29: 22000000 INFO @ Tue, 16 Jun 2020 08:05:32: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:05:32: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:05:32: #1 total tags in treatment: 22495600 INFO @ Tue, 16 Jun 2020 08:05:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:32: #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 08:05:32: #1 tags after filtering in treatment: 22495600 INFO @ Tue, 16 Jun 2020 08:05:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:34: #2 number of paired peaks: 579 WARNING @ Tue, 16 Jun 2020 08:05:34: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:34: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:05:34: #2 alternative fragment length(s) may be 3,57 bps INFO @ Tue, 16 Jun 2020 08:05:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.20_model.r WARNING @ Tue, 16 Jun 2020 08:05:34: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:34: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Tue, 16 Jun 2020 08:05:34: #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 08:05:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.05_summits.bed INFO @ Tue, 16 Jun 2020 08:05:52: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (11591 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.10_summits.bed INFO @ Tue, 16 Jun 2020 08:06:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5699 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007138/SRX1007138.20_summits.bed INFO @ Tue, 16 Jun 2020 08:06:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2212 records, 4 fields): 3 millis CompletedMACS2peakCalling