Job ID = 5790987 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,023,575 reads read : 6,047,150 reads written : 6,047,150 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: 00:02:32 3023575 reads; of these: 3023575 (100.00%) were paired; of these: 220968 (7.31%) aligned concordantly 0 times 2166742 (71.66%) aligned concordantly exactly 1 time 635865 (21.03%) aligned concordantly >1 times ---- 220968 pairs aligned concordantly 0 times; of these: 1145 (0.52%) aligned discordantly 1 time ---- 219823 pairs aligned 0 times concordantly or discordantly; of these: 439646 mates make up the pairs; of these: 417453 (94.95%) aligned 0 times 13992 (3.18%) aligned exactly 1 time 8201 (1.87%) aligned >1 times 93.10% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 49246 / 2784229 = 0.0177 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, 22 Apr 2020 08:15:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 08:15:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:28: 1000000 INFO @ Wed, 22 Apr 2020 08:15:34: 2000000 INFO @ Wed, 22 Apr 2020 08:15:40: 3000000 INFO @ Wed, 22 Apr 2020 08:15:47: 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 @ Wed, 22 Apr 2020 08:15:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 08:15:52: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:52: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:53: 5000000 INFO @ Wed, 22 Apr 2020 08:15:57: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:15:57: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:15:57: #1 total tags in treatment: 2753364 INFO @ Wed, 22 Apr 2020 08:15:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:15:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:15:57: #1 tags after filtering in treatment: 2323982 INFO @ Wed, 22 Apr 2020 08:15:57: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 08:15:57: #1 finished! INFO @ Wed, 22 Apr 2020 08:15:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:15:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:15:57: #2 number of paired peaks: 212 WARNING @ Wed, 22 Apr 2020 08:15:57: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Wed, 22 Apr 2020 08:15:57: start model_add_line... INFO @ Wed, 22 Apr 2020 08:15:57: start X-correlation... INFO @ Wed, 22 Apr 2020 08:15:57: end of X-cor INFO @ Wed, 22 Apr 2020 08:15:57: #2 finished! INFO @ Wed, 22 Apr 2020 08:15:57: #2 predicted fragment length is 127 bps INFO @ Wed, 22 Apr 2020 08:15:57: #2 alternative fragment length(s) may be 2,127,143 bps INFO @ Wed, 22 Apr 2020 08:15:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.05_model.r WARNING @ Wed, 22 Apr 2020 08:15:57: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:15:57: #2 You may need to consider one of the other alternative d(s): 2,127,143 WARNING @ Wed, 22 Apr 2020 08:15:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:15:57: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:15:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:15:59: 1000000 INFO @ Wed, 22 Apr 2020 08:16:02: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:16:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.05_summits.bed INFO @ Wed, 22 Apr 2020 08:16:04: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (585 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:07: 2000000 INFO @ Wed, 22 Apr 2020 08:16:14: 3000000 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, 22 Apr 2020 08:16:21: 4000000 INFO @ Wed, 22 Apr 2020 08:16:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 08:16:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:29: 5000000 INFO @ Wed, 22 Apr 2020 08:16:29: 1000000 INFO @ Wed, 22 Apr 2020 08:16:33: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:33: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:33: #1 total tags in treatment: 2753364 INFO @ Wed, 22 Apr 2020 08:16:33: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:16:33: #1 tags after filtering in treatment: 2323982 INFO @ Wed, 22 Apr 2020 08:16:33: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 08:16:33: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:33: #2 number of paired peaks: 212 WARNING @ Wed, 22 Apr 2020 08:16:33: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Wed, 22 Apr 2020 08:16:33: start model_add_line... INFO @ Wed, 22 Apr 2020 08:16:33: start X-correlation... INFO @ Wed, 22 Apr 2020 08:16:33: end of X-cor INFO @ Wed, 22 Apr 2020 08:16:33: #2 finished! INFO @ Wed, 22 Apr 2020 08:16:33: #2 predicted fragment length is 127 bps INFO @ Wed, 22 Apr 2020 08:16:33: #2 alternative fragment length(s) may be 2,127,143 bps INFO @ Wed, 22 Apr 2020 08:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.10_model.r WARNING @ Wed, 22 Apr 2020 08:16:33: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:16:33: #2 You may need to consider one of the other alternative d(s): 2,127,143 WARNING @ Wed, 22 Apr 2020 08:16:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:16:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:16:37: 2000000 INFO @ Wed, 22 Apr 2020 08:16:39: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:16:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.10_summits.bed INFO @ Wed, 22 Apr 2020 08:16:41: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:44: 3000000 INFO @ Wed, 22 Apr 2020 08:16:51: 4000000 INFO @ Wed, 22 Apr 2020 08:16:59: 5000000 INFO @ Wed, 22 Apr 2020 08:17:02: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:17:02: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:17:02: #1 total tags in treatment: 2753364 INFO @ Wed, 22 Apr 2020 08:17:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:17:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:17:02: #1 tags after filtering in treatment: 2323982 INFO @ Wed, 22 Apr 2020 08:17:02: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 08:17:02: #1 finished! INFO @ Wed, 22 Apr 2020 08:17:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:17:03: #2 number of paired peaks: 212 WARNING @ Wed, 22 Apr 2020 08:17:03: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Wed, 22 Apr 2020 08:17:03: start model_add_line... INFO @ Wed, 22 Apr 2020 08:17:03: start X-correlation... INFO @ Wed, 22 Apr 2020 08:17:03: end of X-cor INFO @ Wed, 22 Apr 2020 08:17:03: #2 finished! INFO @ Wed, 22 Apr 2020 08:17:03: #2 predicted fragment length is 127 bps INFO @ Wed, 22 Apr 2020 08:17:03: #2 alternative fragment length(s) may be 2,127,143 bps INFO @ Wed, 22 Apr 2020 08:17:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.20_model.r WARNING @ Wed, 22 Apr 2020 08:17:03: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:17:03: #2 You may need to consider one of the other alternative d(s): 2,127,143 WARNING @ Wed, 22 Apr 2020 08:17:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:17:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:17:03: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:17:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:17:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:17:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:17:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874486/SRX5874486.20_summits.bed INFO @ Wed, 22 Apr 2020 08:17:10: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。