Job ID = 6507791 SRX = SRX4085368 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T12:56:41 prefetch.2.10.7: 1) Downloading 'SRR7167397'... 2020-06-26T12:56:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:01:02 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:01:02 prefetch.2.10.7: 1) 'SRR7167397' was downloaded successfully Read 23665306 spots for SRR7167397/SRR7167397.sra Written 23665306 spots for SRR7167397/SRR7167397.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: 00:00:01 Multiseed full-index search: 00:15:51 23665306 reads; of these: 23665306 (100.00%) were paired; of these: 6692905 (28.28%) aligned concordantly 0 times 14681500 (62.04%) aligned concordantly exactly 1 time 2290901 (9.68%) aligned concordantly >1 times ---- 6692905 pairs aligned concordantly 0 times; of these: 300871 (4.50%) aligned discordantly 1 time ---- 6392034 pairs aligned 0 times concordantly or discordantly; of these: 12784068 mates make up the pairs; of these: 10307210 (80.63%) aligned 0 times 2164738 (16.93%) aligned exactly 1 time 312120 (2.44%) aligned >1 times 78.22% overall alignment rate Time searching: 00:15:52 Overall time: 00:15:52 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1313845 / 17158559 = 0.0766 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 @ Fri, 26 Jun 2020 22:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.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 @ Fri, 26 Jun 2020 22:29:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:17: 1000000 INFO @ Fri, 26 Jun 2020 22:29:23: 2000000 INFO @ Fri, 26 Jun 2020 22:29:28: 3000000 INFO @ Fri, 26 Jun 2020 22:29:34: 4000000 INFO @ Fri, 26 Jun 2020 22:29:39: 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 @ Fri, 26 Jun 2020 22:29:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.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 @ Fri, 26 Jun 2020 22:29:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:45: 6000000 INFO @ Fri, 26 Jun 2020 22:29:48: 1000000 INFO @ Fri, 26 Jun 2020 22:29:51: 7000000 INFO @ Fri, 26 Jun 2020 22:29:54: 2000000 INFO @ Fri, 26 Jun 2020 22:29:57: 8000000 INFO @ Fri, 26 Jun 2020 22:30:00: 3000000 INFO @ Fri, 26 Jun 2020 22:30:03: 9000000 INFO @ Fri, 26 Jun 2020 22:30:06: 4000000 INFO @ Fri, 26 Jun 2020 22:30:09: 10000000 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 @ Fri, 26 Jun 2020 22:30:12: 5000000 INFO @ Fri, 26 Jun 2020 22:30:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.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 @ Fri, 26 Jun 2020 22:30:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:30:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:30:15: 11000000 INFO @ Fri, 26 Jun 2020 22:30:18: 6000000 INFO @ Fri, 26 Jun 2020 22:30:18: 1000000 INFO @ Fri, 26 Jun 2020 22:30:21: 12000000 INFO @ Fri, 26 Jun 2020 22:30:25: 7000000 INFO @ Fri, 26 Jun 2020 22:30:25: 2000000 INFO @ Fri, 26 Jun 2020 22:30:28: 13000000 INFO @ Fri, 26 Jun 2020 22:30:31: 8000000 INFO @ Fri, 26 Jun 2020 22:30:31: 3000000 INFO @ Fri, 26 Jun 2020 22:30:34: 14000000 INFO @ Fri, 26 Jun 2020 22:30:38: 9000000 INFO @ Fri, 26 Jun 2020 22:30:38: 4000000 INFO @ Fri, 26 Jun 2020 22:30:40: 15000000 INFO @ Fri, 26 Jun 2020 22:30:44: 10000000 INFO @ Fri, 26 Jun 2020 22:30:44: 5000000 INFO @ Fri, 26 Jun 2020 22:30:47: 16000000 INFO @ Fri, 26 Jun 2020 22:30:51: 11000000 INFO @ Fri, 26 Jun 2020 22:30:51: 6000000 INFO @ Fri, 26 Jun 2020 22:30:53: 17000000 INFO @ Fri, 26 Jun 2020 22:30:57: 12000000 INFO @ Fri, 26 Jun 2020 22:30:57: 7000000 INFO @ Fri, 26 Jun 2020 22:31:00: 18000000 INFO @ Fri, 26 Jun 2020 22:31:04: 13000000 INFO @ Fri, 26 Jun 2020 22:31:04: 8000000 INFO @ Fri, 26 Jun 2020 22:31:06: 19000000 INFO @ Fri, 26 Jun 2020 22:31:10: 14000000 INFO @ Fri, 26 Jun 2020 22:31:10: 9000000 INFO @ Fri, 26 Jun 2020 22:31:12: 20000000 INFO @ Fri, 26 Jun 2020 22:31:17: 15000000 INFO @ Fri, 26 Jun 2020 22:31:18: 10000000 INFO @ Fri, 26 Jun 2020 22:31:19: 21000000 INFO @ Fri, 26 Jun 2020 22:31:24: 16000000 INFO @ Fri, 26 Jun 2020 22:31:24: 11000000 INFO @ Fri, 26 Jun 2020 22:31:26: 22000000 INFO @ Fri, 26 Jun 2020 22:31:30: 17000000 INFO @ Fri, 26 Jun 2020 22:31:31: 12000000 INFO @ Fri, 26 Jun 2020 22:31:32: 23000000 INFO @ Fri, 26 Jun 2020 22:31:37: 18000000 INFO @ Fri, 26 Jun 2020 22:31:38: 13000000 INFO @ Fri, 26 Jun 2020 22:31:39: 24000000 INFO @ Fri, 26 Jun 2020 22:31:44: 19000000 INFO @ Fri, 26 Jun 2020 22:31:45: 14000000 INFO @ Fri, 26 Jun 2020 22:31:45: 25000000 INFO @ Fri, 26 Jun 2020 22:31:51: 20000000 INFO @ Fri, 26 Jun 2020 22:31:52: 26000000 INFO @ Fri, 26 Jun 2020 22:31:52: 15000000 INFO @ Fri, 26 Jun 2020 22:31:57: 21000000 INFO @ Fri, 26 Jun 2020 22:31:58: 27000000 INFO @ Fri, 26 Jun 2020 22:31:59: 16000000 INFO @ Fri, 26 Jun 2020 22:32:04: 22000000 INFO @ Fri, 26 Jun 2020 22:32:04: 28000000 INFO @ Fri, 26 Jun 2020 22:32:05: 17000000 INFO @ Fri, 26 Jun 2020 22:32:10: 23000000 INFO @ Fri, 26 Jun 2020 22:32:11: 29000000 INFO @ Fri, 26 Jun 2020 22:32:12: 18000000 INFO @ Fri, 26 Jun 2020 22:32:17: 24000000 INFO @ Fri, 26 Jun 2020 22:32:17: 30000000 INFO @ Fri, 26 Jun 2020 22:32:18: 19000000 INFO @ Fri, 26 Jun 2020 22:32:23: 31000000 INFO @ Fri, 26 Jun 2020 22:32:23: 25000000 INFO @ Fri, 26 Jun 2020 22:32:25: 20000000 INFO @ Fri, 26 Jun 2020 22:32:30: 32000000 INFO @ Fri, 26 Jun 2020 22:32:30: 26000000 INFO @ Fri, 26 Jun 2020 22:32:31: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:32:36: 33000000 INFO @ Fri, 26 Jun 2020 22:32:36: 27000000 INFO @ Fri, 26 Jun 2020 22:32:38: 22000000 INFO @ Fri, 26 Jun 2020 22:32:42: 34000000 INFO @ Fri, 26 Jun 2020 22:32:43: 28000000 INFO @ Fri, 26 Jun 2020 22:32:44: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:32:44: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:32:44: #1 total tags in treatment: 15673080 INFO @ Fri, 26 Jun 2020 22:32:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:32:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:32:44: 23000000 INFO @ Fri, 26 Jun 2020 22:32:44: #1 tags after filtering in treatment: 13532482 INFO @ Fri, 26 Jun 2020 22:32:44: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 22:32:44: #1 finished! INFO @ Fri, 26 Jun 2020 22:32:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:32:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:32:45: #2 number of paired peaks: 269 WARNING @ Fri, 26 Jun 2020 22:32:45: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Fri, 26 Jun 2020 22:32:45: start model_add_line... INFO @ Fri, 26 Jun 2020 22:32:45: start X-correlation... INFO @ Fri, 26 Jun 2020 22:32:45: end of X-cor INFO @ Fri, 26 Jun 2020 22:32:45: #2 finished! INFO @ Fri, 26 Jun 2020 22:32:45: #2 predicted fragment length is 98 bps INFO @ Fri, 26 Jun 2020 22:32:45: #2 alternative fragment length(s) may be 4,98 bps INFO @ Fri, 26 Jun 2020 22:32:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.05_model.r WARNING @ Fri, 26 Jun 2020 22:32:45: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:32:45: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Fri, 26 Jun 2020 22:32:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:32:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:32:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:32:49: 29000000 INFO @ Fri, 26 Jun 2020 22:32:50: 24000000 INFO @ Fri, 26 Jun 2020 22:32:55: 30000000 INFO @ Fri, 26 Jun 2020 22:32:57: 25000000 INFO @ Fri, 26 Jun 2020 22:33:02: 31000000 INFO @ Fri, 26 Jun 2020 22:33:03: 26000000 INFO @ Fri, 26 Jun 2020 22:33:08: 32000000 INFO @ Fri, 26 Jun 2020 22:33:10: 27000000 INFO @ Fri, 26 Jun 2020 22:33:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:33:14: 33000000 INFO @ Fri, 26 Jun 2020 22:33:16: 28000000 INFO @ Fri, 26 Jun 2020 22:33:20: 34000000 INFO @ Fri, 26 Jun 2020 22:33:23: 29000000 INFO @ Fri, 26 Jun 2020 22:33:23: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:33:23: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:33:23: #1 total tags in treatment: 15673080 INFO @ Fri, 26 Jun 2020 22:33:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:33:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:33:23: #1 tags after filtering in treatment: 13532482 INFO @ Fri, 26 Jun 2020 22:33:23: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 22:33:23: #1 finished! INFO @ Fri, 26 Jun 2020 22:33:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:33:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:33:24: #2 number of paired peaks: 269 WARNING @ Fri, 26 Jun 2020 22:33:24: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Fri, 26 Jun 2020 22:33:24: start model_add_line... INFO @ Fri, 26 Jun 2020 22:33:24: start X-correlation... INFO @ Fri, 26 Jun 2020 22:33:24: end of X-cor INFO @ Fri, 26 Jun 2020 22:33:24: #2 finished! INFO @ Fri, 26 Jun 2020 22:33:24: #2 predicted fragment length is 98 bps INFO @ Fri, 26 Jun 2020 22:33:24: #2 alternative fragment length(s) may be 4,98 bps INFO @ Fri, 26 Jun 2020 22:33:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.10_model.r WARNING @ Fri, 26 Jun 2020 22:33:24: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:33:24: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Fri, 26 Jun 2020 22:33:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:33:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:33:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:33:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:33:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:33:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.05_summits.bed INFO @ Fri, 26 Jun 2020 22:33:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3666 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:33:29: 30000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:33:34: 31000000 INFO @ Fri, 26 Jun 2020 22:33:40: 32000000 INFO @ Fri, 26 Jun 2020 22:33:46: 33000000 INFO @ Fri, 26 Jun 2020 22:33:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:33:51: 34000000 INFO @ Fri, 26 Jun 2020 22:33:54: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:33:54: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:33:54: #1 total tags in treatment: 15673080 INFO @ Fri, 26 Jun 2020 22:33:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:33:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:33:54: #1 tags after filtering in treatment: 13532482 INFO @ Fri, 26 Jun 2020 22:33:54: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 22:33:54: #1 finished! INFO @ Fri, 26 Jun 2020 22:33:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:33:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:33:55: #2 number of paired peaks: 269 WARNING @ Fri, 26 Jun 2020 22:33:55: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Fri, 26 Jun 2020 22:33:55: start model_add_line... INFO @ Fri, 26 Jun 2020 22:33:55: start X-correlation... INFO @ Fri, 26 Jun 2020 22:33:55: end of X-cor INFO @ Fri, 26 Jun 2020 22:33:55: #2 finished! INFO @ Fri, 26 Jun 2020 22:33:55: #2 predicted fragment length is 98 bps INFO @ Fri, 26 Jun 2020 22:33:55: #2 alternative fragment length(s) may be 4,98 bps INFO @ Fri, 26 Jun 2020 22:33:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.20_model.r WARNING @ Fri, 26 Jun 2020 22:33:55: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:33:55: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Fri, 26 Jun 2020 22:33:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:33:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:33:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:34:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:34:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:34:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.10_summits.bed INFO @ Fri, 26 Jun 2020 22:34:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2312 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:34:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:34:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:34:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:34:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085368/SRX4085368.20_summits.bed INFO @ Fri, 26 Jun 2020 22:34:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1139 records, 4 fields): 62 millis CompletedMACS2peakCalling