Job ID = 6507741 SRX = SRX2011719 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:39:12 prefetch.2.10.7: 1) Downloading 'SRR4017961'... 2020-06-26T13:39:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:45:17 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:45:17 prefetch.2.10.7: 1) 'SRR4017961' was downloaded successfully Read 10994649 spots for SRR4017961/SRR4017961.sra Written 10994649 spots for SRR4017961/SRR4017961.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:53 10994649 reads; of these: 10994649 (100.00%) were paired; of these: 1192290 (10.84%) aligned concordantly 0 times 8504508 (77.35%) aligned concordantly exactly 1 time 1297851 (11.80%) aligned concordantly >1 times ---- 1192290 pairs aligned concordantly 0 times; of these: 879650 (73.78%) aligned discordantly 1 time ---- 312640 pairs aligned 0 times concordantly or discordantly; of these: 625280 mates make up the pairs; of these: 225763 (36.11%) aligned 0 times 182617 (29.21%) aligned exactly 1 time 216900 (34.69%) aligned >1 times 98.97% overall alignment rate Time searching: 00:17:54 Overall time: 00:17:54 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_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] 797163 / 10578221 = 0.0754 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 23:15:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.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 23:15:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:15:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:15:42: 1000000 INFO @ Fri, 26 Jun 2020 23:15:48: 2000000 INFO @ Fri, 26 Jun 2020 23:15:55: 3000000 INFO @ Fri, 26 Jun 2020 23:16:02: 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 @ Fri, 26 Jun 2020 23:16:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.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 23:16:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:16:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:16:09: 5000000 INFO @ Fri, 26 Jun 2020 23:16:12: 1000000 INFO @ Fri, 26 Jun 2020 23:16:16: 6000000 INFO @ Fri, 26 Jun 2020 23:16:20: 2000000 INFO @ Fri, 26 Jun 2020 23:16:23: 7000000 INFO @ Fri, 26 Jun 2020 23:16:27: 3000000 INFO @ Fri, 26 Jun 2020 23:16:31: 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 @ Fri, 26 Jun 2020 23:16:34: 4000000 INFO @ Fri, 26 Jun 2020 23:16:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.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 23:16:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:16:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:16:38: 9000000 INFO @ Fri, 26 Jun 2020 23:16:42: 5000000 INFO @ Fri, 26 Jun 2020 23:16:42: 1000000 INFO @ Fri, 26 Jun 2020 23:16:45: 10000000 INFO @ Fri, 26 Jun 2020 23:16:49: 6000000 INFO @ Fri, 26 Jun 2020 23:16:50: 2000000 INFO @ Fri, 26 Jun 2020 23:16:53: 11000000 INFO @ Fri, 26 Jun 2020 23:16:57: 7000000 INFO @ Fri, 26 Jun 2020 23:16:57: 3000000 INFO @ Fri, 26 Jun 2020 23:17:00: 12000000 INFO @ Fri, 26 Jun 2020 23:17:04: 8000000 INFO @ Fri, 26 Jun 2020 23:17:05: 4000000 INFO @ Fri, 26 Jun 2020 23:17:08: 13000000 INFO @ Fri, 26 Jun 2020 23:17:12: 9000000 INFO @ Fri, 26 Jun 2020 23:17:12: 5000000 INFO @ Fri, 26 Jun 2020 23:17:15: 14000000 INFO @ Fri, 26 Jun 2020 23:17:19: 10000000 INFO @ Fri, 26 Jun 2020 23:17:20: 6000000 INFO @ Fri, 26 Jun 2020 23:17:23: 15000000 INFO @ Fri, 26 Jun 2020 23:17:27: 11000000 INFO @ Fri, 26 Jun 2020 23:17:27: 7000000 INFO @ Fri, 26 Jun 2020 23:17:31: 16000000 INFO @ Fri, 26 Jun 2020 23:17:35: 12000000 INFO @ Fri, 26 Jun 2020 23:17:35: 8000000 INFO @ Fri, 26 Jun 2020 23:17:38: 17000000 INFO @ Fri, 26 Jun 2020 23:17:42: 13000000 INFO @ Fri, 26 Jun 2020 23:17:43: 9000000 INFO @ Fri, 26 Jun 2020 23:17:46: 18000000 INFO @ Fri, 26 Jun 2020 23:17:50: 14000000 INFO @ Fri, 26 Jun 2020 23:17:51: 10000000 INFO @ Fri, 26 Jun 2020 23:17:54: 19000000 INFO @ Fri, 26 Jun 2020 23:17:57: 15000000 INFO @ Fri, 26 Jun 2020 23:17:58: 11000000 INFO @ Fri, 26 Jun 2020 23:18:01: 20000000 INFO @ Fri, 26 Jun 2020 23:18:03: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:18:03: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:18:03: #1 total tags in treatment: 9032050 INFO @ Fri, 26 Jun 2020 23:18:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:18:03: #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 23:18:03: #1 tags after filtering in treatment: 8400074 INFO @ Fri, 26 Jun 2020 23:18:03: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 23:18:03: #1 finished! INFO @ Fri, 26 Jun 2020 23:18:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:18:03: #2 number of paired peaks: 361 WARNING @ Fri, 26 Jun 2020 23:18:03: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 26 Jun 2020 23:18:03: start model_add_line... INFO @ Fri, 26 Jun 2020 23:18:03: start X-correlation... INFO @ Fri, 26 Jun 2020 23:18:03: end of X-cor INFO @ Fri, 26 Jun 2020 23:18:03: #2 finished! INFO @ Fri, 26 Jun 2020 23:18:03: #2 predicted fragment length is 162 bps INFO @ Fri, 26 Jun 2020 23:18:03: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 26 Jun 2020 23:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.05_model.r WARNING @ Fri, 26 Jun 2020 23:18:03: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:18:03: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Fri, 26 Jun 2020 23:18:03: #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 23:18:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:18:05: 16000000 INFO @ Fri, 26 Jun 2020 23:18:06: 12000000 INFO @ Fri, 26 Jun 2020 23:18:13: 17000000 INFO @ Fri, 26 Jun 2020 23:18:13: 13000000 INFO @ Fri, 26 Jun 2020 23:18:20: 18000000 INFO @ Fri, 26 Jun 2020 23:18:21: 14000000 INFO @ Fri, 26 Jun 2020 23:18:23: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:18:28: 19000000 INFO @ Fri, 26 Jun 2020 23:18:29: 15000000 INFO @ Fri, 26 Jun 2020 23:18:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:18:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:18:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.05_summits.bed INFO @ Fri, 26 Jun 2020 23:18:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (364 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:18:35: 20000000 INFO @ Fri, 26 Jun 2020 23:18:36: 16000000 INFO @ Fri, 26 Jun 2020 23:18:37: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:18:37: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:18:37: #1 total tags in treatment: 9032050 INFO @ Fri, 26 Jun 2020 23:18:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:18:37: #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 23:18:37: #1 tags after filtering in treatment: 8400074 INFO @ Fri, 26 Jun 2020 23:18:37: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 23:18:37: #1 finished! INFO @ Fri, 26 Jun 2020 23:18:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:18:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:18:37: #2 number of paired peaks: 361 WARNING @ Fri, 26 Jun 2020 23:18:37: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 26 Jun 2020 23:18:37: start model_add_line... INFO @ Fri, 26 Jun 2020 23:18:37: start X-correlation... INFO @ Fri, 26 Jun 2020 23:18:37: end of X-cor INFO @ Fri, 26 Jun 2020 23:18:37: #2 finished! INFO @ Fri, 26 Jun 2020 23:18:37: #2 predicted fragment length is 162 bps INFO @ Fri, 26 Jun 2020 23:18:37: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 26 Jun 2020 23:18:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.10_model.r WARNING @ Fri, 26 Jun 2020 23:18:37: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:18:37: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Fri, 26 Jun 2020 23:18:37: #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 23:18:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:18:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:18:43: 17000000 INFO @ Fri, 26 Jun 2020 23:18:51: 18000000 INFO @ Fri, 26 Jun 2020 23:18:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:18:58: 19000000 INFO @ Fri, 26 Jun 2020 23:19:05: 20000000 INFO @ Fri, 26 Jun 2020 23:19:06: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:19:06: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:19:06: #1 total tags in treatment: 9032050 INFO @ Fri, 26 Jun 2020 23:19:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:19:06: #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 23:19:06: #1 tags after filtering in treatment: 8400074 INFO @ Fri, 26 Jun 2020 23:19:06: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 23:19:06: #1 finished! INFO @ Fri, 26 Jun 2020 23:19:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:19:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:19:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:19:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:19:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.10_summits.bed INFO @ Fri, 26 Jun 2020 23:19:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (282 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:19:07: #2 number of paired peaks: 361 WARNING @ Fri, 26 Jun 2020 23:19:07: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 26 Jun 2020 23:19:07: start model_add_line... INFO @ Fri, 26 Jun 2020 23:19:07: start X-correlation... INFO @ Fri, 26 Jun 2020 23:19:07: end of X-cor INFO @ Fri, 26 Jun 2020 23:19:07: #2 finished! INFO @ Fri, 26 Jun 2020 23:19:07: #2 predicted fragment length is 162 bps INFO @ Fri, 26 Jun 2020 23:19:07: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 26 Jun 2020 23:19:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.20_model.r WARNING @ Fri, 26 Jun 2020 23:19:07: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:19:07: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Fri, 26 Jun 2020 23:19:07: #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 23:19:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:19:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:19:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:19:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:19:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:19:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011719/SRX2011719.20_summits.bed INFO @ Fri, 26 Jun 2020 23:19:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 1 millis CompletedMACS2peakCalling