Job ID = 5720175 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,089,929 reads read : 24,179,858 reads written : 24,179,858 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:30:44 12089929 reads; of these: 12089929 (100.00%) were paired; of these: 6233865 (51.56%) aligned concordantly 0 times 4826647 (39.92%) aligned concordantly exactly 1 time 1029417 (8.51%) aligned concordantly >1 times ---- 6233865 pairs aligned concordantly 0 times; of these: 3142720 (50.41%) aligned discordantly 1 time ---- 3091145 pairs aligned 0 times concordantly or discordantly; of these: 6182290 mates make up the pairs; of these: 5145636 (83.23%) aligned 0 times 390263 (6.31%) aligned exactly 1 time 646391 (10.46%) aligned >1 times 78.72% overall alignment rate Time searching: 00:30:44 Overall time: 00:30:44 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] 562963 / 8843362 = 0.0637 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 @ Wed, 15 Apr 2020 22:21:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.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 @ Wed, 15 Apr 2020 22:21:18: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:21:18: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:21:29: 1000000 INFO @ Wed, 15 Apr 2020 22:21:39: 2000000 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 @ Wed, 15 Apr 2020 22:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.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 @ Wed, 15 Apr 2020 22:21:47: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:21:47: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:21:50: 3000000 INFO @ Wed, 15 Apr 2020 22:21:59: 1000000 INFO @ Wed, 15 Apr 2020 22:22:01: 4000000 INFO @ Wed, 15 Apr 2020 22:22:10: 2000000 INFO @ Wed, 15 Apr 2020 22:22:12: 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 @ Wed, 15 Apr 2020 22:22:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.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 @ Wed, 15 Apr 2020 22:22:18: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:22:18: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:22:21: 3000000 INFO @ Wed, 15 Apr 2020 22:22:23: 6000000 INFO @ Wed, 15 Apr 2020 22:22:29: 1000000 INFO @ Wed, 15 Apr 2020 22:22:33: 4000000 INFO @ Wed, 15 Apr 2020 22:22:34: 7000000 INFO @ Wed, 15 Apr 2020 22:22:41: 2000000 INFO @ Wed, 15 Apr 2020 22:22:45: 5000000 INFO @ Wed, 15 Apr 2020 22:22:45: 8000000 INFO @ Wed, 15 Apr 2020 22:22:54: 3000000 INFO @ Wed, 15 Apr 2020 22:22:57: 9000000 INFO @ Wed, 15 Apr 2020 22:22:58: 6000000 INFO @ Wed, 15 Apr 2020 22:23:08: 4000000 INFO @ Wed, 15 Apr 2020 22:23:11: 10000000 INFO @ Wed, 15 Apr 2020 22:23:12: 7000000 INFO @ Wed, 15 Apr 2020 22:23:22: 5000000 INFO @ Wed, 15 Apr 2020 22:23:23: 11000000 INFO @ Wed, 15 Apr 2020 22:23:26: 8000000 INFO @ Wed, 15 Apr 2020 22:23:35: 12000000 INFO @ Wed, 15 Apr 2020 22:23:36: 6000000 INFO @ Wed, 15 Apr 2020 22:23:40: 9000000 INFO @ Wed, 15 Apr 2020 22:23:46: 13000000 INFO @ Wed, 15 Apr 2020 22:23:50: 7000000 INFO @ Wed, 15 Apr 2020 22:23:55: 10000000 INFO @ Wed, 15 Apr 2020 22:23:58: 14000000 INFO @ Wed, 15 Apr 2020 22:24:05: 8000000 INFO @ Wed, 15 Apr 2020 22:24:08: 11000000 INFO @ Wed, 15 Apr 2020 22:24:09: 15000000 INFO @ Wed, 15 Apr 2020 22:24:18: 9000000 INFO @ Wed, 15 Apr 2020 22:24:20: 16000000 INFO @ Wed, 15 Apr 2020 22:24:22: 12000000 INFO @ Wed, 15 Apr 2020 22:24:31: 17000000 INFO @ Wed, 15 Apr 2020 22:24:31: 10000000 INFO @ Wed, 15 Apr 2020 22:24:35: 13000000 INFO @ Wed, 15 Apr 2020 22:24:41: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 22:24:41: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 22:24:41: #1 total tags in treatment: 5462948 INFO @ Wed, 15 Apr 2020 22:24:41: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:24:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:24:41: #1 tags after filtering in treatment: 4950534 INFO @ Wed, 15 Apr 2020 22:24:41: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 15 Apr 2020 22:24:41: #1 finished! INFO @ Wed, 15 Apr 2020 22:24:41: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:24:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:24:41: #2 number of paired peaks: 389 WARNING @ Wed, 15 Apr 2020 22:24:41: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Wed, 15 Apr 2020 22:24:41: start model_add_line... INFO @ Wed, 15 Apr 2020 22:24:42: start X-correlation... INFO @ Wed, 15 Apr 2020 22:24:42: end of X-cor INFO @ Wed, 15 Apr 2020 22:24:42: #2 finished! INFO @ Wed, 15 Apr 2020 22:24:42: #2 predicted fragment length is 214 bps INFO @ Wed, 15 Apr 2020 22:24:42: #2 alternative fragment length(s) may be 214,230 bps INFO @ Wed, 15 Apr 2020 22:24:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.05_model.r WARNING @ Wed, 15 Apr 2020 22:24:42: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:24:42: #2 You may need to consider one of the other alternative d(s): 214,230 WARNING @ Wed, 15 Apr 2020 22:24:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:24:42: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:24:43: 11000000 INFO @ Wed, 15 Apr 2020 22:24:46: 14000000 INFO @ Wed, 15 Apr 2020 22:24:52: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:24:55: 12000000 INFO @ Wed, 15 Apr 2020 22:24:58: 15000000 INFO @ Wed, 15 Apr 2020 22:24:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:24:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:24:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.05_summits.bed INFO @ Wed, 15 Apr 2020 22:24:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:25:08: 13000000 INFO @ Wed, 15 Apr 2020 22:25:11: 16000000 INFO @ Wed, 15 Apr 2020 22:25:20: 14000000 INFO @ Wed, 15 Apr 2020 22:25:23: 17000000 INFO @ Wed, 15 Apr 2020 22:25:34: 15000000 INFO @ Wed, 15 Apr 2020 22:25:35: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 22:25:35: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 22:25:35: #1 total tags in treatment: 5462948 INFO @ Wed, 15 Apr 2020 22:25:35: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:25:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:25:35: #1 tags after filtering in treatment: 4950534 INFO @ Wed, 15 Apr 2020 22:25:35: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 15 Apr 2020 22:25:35: #1 finished! INFO @ Wed, 15 Apr 2020 22:25:35: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:25:36: #2 number of paired peaks: 389 WARNING @ Wed, 15 Apr 2020 22:25:36: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Wed, 15 Apr 2020 22:25:36: start model_add_line... INFO @ Wed, 15 Apr 2020 22:25:36: start X-correlation... INFO @ Wed, 15 Apr 2020 22:25:36: end of X-cor INFO @ Wed, 15 Apr 2020 22:25:36: #2 finished! INFO @ Wed, 15 Apr 2020 22:25:36: #2 predicted fragment length is 214 bps INFO @ Wed, 15 Apr 2020 22:25:36: #2 alternative fragment length(s) may be 214,230 bps INFO @ Wed, 15 Apr 2020 22:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.10_model.r WARNING @ Wed, 15 Apr 2020 22:25:36: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:25:36: #2 You may need to consider one of the other alternative d(s): 214,230 WARNING @ Wed, 15 Apr 2020 22:25:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:25:36: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:25:45: 16000000 INFO @ Wed, 15 Apr 2020 22:25:47: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:25:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:25:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:25:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.10_summits.bed INFO @ Wed, 15 Apr 2020 22:25:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (247 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:25:56: 17000000 INFO @ Wed, 15 Apr 2020 22:26:06: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 22:26:06: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 22:26:06: #1 total tags in treatment: 5462948 INFO @ Wed, 15 Apr 2020 22:26:06: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:26:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:26:06: #1 tags after filtering in treatment: 4950534 INFO @ Wed, 15 Apr 2020 22:26:06: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 15 Apr 2020 22:26:06: #1 finished! INFO @ Wed, 15 Apr 2020 22:26:06: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:26:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:26:07: #2 number of paired peaks: 389 WARNING @ Wed, 15 Apr 2020 22:26:07: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Wed, 15 Apr 2020 22:26:07: start model_add_line... INFO @ Wed, 15 Apr 2020 22:26:07: start X-correlation... INFO @ Wed, 15 Apr 2020 22:26:07: end of X-cor INFO @ Wed, 15 Apr 2020 22:26:07: #2 finished! INFO @ Wed, 15 Apr 2020 22:26:07: #2 predicted fragment length is 214 bps INFO @ Wed, 15 Apr 2020 22:26:07: #2 alternative fragment length(s) may be 214,230 bps INFO @ Wed, 15 Apr 2020 22:26:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.20_model.r WARNING @ Wed, 15 Apr 2020 22:26:07: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:26:07: #2 You may need to consider one of the other alternative d(s): 214,230 WARNING @ Wed, 15 Apr 2020 22:26:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:26:07: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:26:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:26:18: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619546/SRX6619546.20_summits.bed INFO @ Wed, 15 Apr 2020 22:26:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (166 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。