Job ID = 5790858 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,204,126 reads read : 4,408,252 reads written : 4,408,252 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: 00:01:07 2204126 reads; of these: 2204126 (100.00%) were paired; of these: 38735 (1.76%) aligned concordantly 0 times 1902946 (86.34%) aligned concordantly exactly 1 time 262445 (11.91%) aligned concordantly >1 times ---- 38735 pairs aligned concordantly 0 times; of these: 3453 (8.91%) aligned discordantly 1 time ---- 35282 pairs aligned 0 times concordantly or discordantly; of these: 70564 mates make up the pairs; of these: 55892 (79.21%) aligned 0 times 11553 (16.37%) aligned exactly 1 time 3119 (4.42%) aligned >1 times 98.73% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 40047 / 2166088 = 0.0185 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 07:59:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.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 07:59:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:59:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:59:42: 1000000 INFO @ Wed, 22 Apr 2020 07:59:49: 2000000 INFO @ Wed, 22 Apr 2020 07:59:55: 3000000 INFO @ Wed, 22 Apr 2020 08:00:01: 4000000 INFO @ Wed, 22 Apr 2020 08:00:02: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:00:02: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:00:02: #1 total tags in treatment: 2125355 INFO @ Wed, 22 Apr 2020 08:00:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:00:02: #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 08:00:02: #1 tags after filtering in treatment: 1900514 INFO @ Wed, 22 Apr 2020 08:00:02: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:00:02: #1 finished! INFO @ Wed, 22 Apr 2020 08:00:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:00:03: #2 number of paired peaks: 111 WARNING @ Wed, 22 Apr 2020 08:00:03: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 22 Apr 2020 08:00:03: start model_add_line... INFO @ Wed, 22 Apr 2020 08:00:03: start X-correlation... INFO @ Wed, 22 Apr 2020 08:00:03: end of X-cor INFO @ Wed, 22 Apr 2020 08:00:03: #2 finished! INFO @ Wed, 22 Apr 2020 08:00:03: #2 predicted fragment length is 71 bps INFO @ Wed, 22 Apr 2020 08:00:03: #2 alternative fragment length(s) may be 3,10,25,71 bps INFO @ Wed, 22 Apr 2020 08:00:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.05_model.r WARNING @ Wed, 22 Apr 2020 08:00:03: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:00:03: #2 You may need to consider one of the other alternative d(s): 3,10,25,71 WARNING @ Wed, 22 Apr 2020 08:00:03: #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 08:00:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:00:03: #3 Pre-compute pvalue-qvalue table... 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 08:00:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.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 08:00:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:00:06: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.05_summits.bed INFO @ Wed, 22 Apr 2020 08:00:09: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (716 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:00:11: 1000000 INFO @ Wed, 22 Apr 2020 08:00:17: 2000000 INFO @ Wed, 22 Apr 2020 08:00:22: 3000000 INFO @ Wed, 22 Apr 2020 08:00:27: 4000000 INFO @ Wed, 22 Apr 2020 08:00:28: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:00:28: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:00:28: #1 total tags in treatment: 2125355 INFO @ Wed, 22 Apr 2020 08:00:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:00:28: #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 08:00:28: #1 tags after filtering in treatment: 1900514 INFO @ Wed, 22 Apr 2020 08:00:28: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:00:28: #1 finished! INFO @ Wed, 22 Apr 2020 08:00:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:00:28: #2 number of paired peaks: 111 WARNING @ Wed, 22 Apr 2020 08:00:28: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 22 Apr 2020 08:00:28: start model_add_line... INFO @ Wed, 22 Apr 2020 08:00:28: start X-correlation... INFO @ Wed, 22 Apr 2020 08:00:28: end of X-cor INFO @ Wed, 22 Apr 2020 08:00:28: #2 finished! INFO @ Wed, 22 Apr 2020 08:00:28: #2 predicted fragment length is 71 bps INFO @ Wed, 22 Apr 2020 08:00:28: #2 alternative fragment length(s) may be 3,10,25,71 bps INFO @ Wed, 22 Apr 2020 08:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.10_model.r WARNING @ Wed, 22 Apr 2020 08:00:28: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:00:28: #2 You may need to consider one of the other alternative d(s): 3,10,25,71 WARNING @ Wed, 22 Apr 2020 08:00:28: #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 08:00:28: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:00:32: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.10_summits.bed INFO @ Wed, 22 Apr 2020 08:00:34: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (305 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 08:00:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.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 08:00:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:00:43: 1000000 INFO @ Wed, 22 Apr 2020 08:00:50: 2000000 INFO @ Wed, 22 Apr 2020 08:00:57: 3000000 INFO @ Wed, 22 Apr 2020 08:01:03: 4000000 INFO @ Wed, 22 Apr 2020 08:01:05: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:01:05: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:01:05: #1 total tags in treatment: 2125355 INFO @ Wed, 22 Apr 2020 08:01:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:01:05: #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 08:01:05: #1 tags after filtering in treatment: 1900514 INFO @ Wed, 22 Apr 2020 08:01:05: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:01:05: #1 finished! INFO @ Wed, 22 Apr 2020 08:01:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:01:05: #2 number of paired peaks: 111 WARNING @ Wed, 22 Apr 2020 08:01:05: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 22 Apr 2020 08:01:05: start model_add_line... INFO @ Wed, 22 Apr 2020 08:01:05: start X-correlation... INFO @ Wed, 22 Apr 2020 08:01:05: end of X-cor INFO @ Wed, 22 Apr 2020 08:01:05: #2 finished! INFO @ Wed, 22 Apr 2020 08:01:05: #2 predicted fragment length is 71 bps INFO @ Wed, 22 Apr 2020 08:01:05: #2 alternative fragment length(s) may be 3,10,25,71 bps INFO @ Wed, 22 Apr 2020 08:01:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.20_model.r WARNING @ Wed, 22 Apr 2020 08:01:05: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:01:05: #2 You may need to consider one of the other alternative d(s): 3,10,25,71 WARNING @ Wed, 22 Apr 2020 08:01:05: #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 08:01:05: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:01:05: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:01:09: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:01:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:01:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:01:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521506/SRX5521506.20_summits.bed INFO @ Wed, 22 Apr 2020 08:01:11: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。