Job ID = 14521913 SRX = ERX4439593 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3537948 spots for ERR4501522/ERR4501522.sra Written 3537948 spots for ERR4501522/ERR4501522.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: 00:00:00 Multiseed full-index search: 00:02:43 3537948 reads; of these: 3537948 (100.00%) were paired; of these: 1044852 (29.53%) aligned concordantly 0 times 2235955 (63.20%) aligned concordantly exactly 1 time 257141 (7.27%) aligned concordantly >1 times ---- 1044852 pairs aligned concordantly 0 times; of these: 443534 (42.45%) aligned discordantly 1 time ---- 601318 pairs aligned 0 times concordantly or discordantly; of these: 1202636 mates make up the pairs; of these: 1037825 (86.30%) aligned 0 times 61670 (5.13%) aligned exactly 1 time 103141 (8.58%) aligned >1 times 85.33% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 38116 / 2907414 = 0.0131 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.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 @ Sat, 15 Jan 2022 21:56:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:56:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:56:45: 1000000 INFO @ Sat, 15 Jan 2022 21:56:51: 2000000 INFO @ Sat, 15 Jan 2022 21:56:58: 3000000 INFO @ Sat, 15 Jan 2022 21:57:04: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.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 @ Sat, 15 Jan 2022 21:57:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:57:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:57:11: 5000000 INFO @ Sat, 15 Jan 2022 21:57:15: 1000000 INFO @ Sat, 15 Jan 2022 21:57:17: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:57:17: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:57:17: #1 total tags in treatment: 2462298 INFO @ Sat, 15 Jan 2022 21:57:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:57:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:57:17: #1 tags after filtering in treatment: 2224753 INFO @ Sat, 15 Jan 2022 21:57:17: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:57:17: #1 finished! INFO @ Sat, 15 Jan 2022 21:57:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:57:17: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 21:57:17: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 21:57:17: start model_add_line... INFO @ Sat, 15 Jan 2022 21:57:17: start X-correlation... INFO @ Sat, 15 Jan 2022 21:57:17: end of X-cor INFO @ Sat, 15 Jan 2022 21:57:17: #2 finished! INFO @ Sat, 15 Jan 2022 21:57:17: #2 predicted fragment length is 159 bps INFO @ Sat, 15 Jan 2022 21:57:17: #2 alternative fragment length(s) may be 1,138,159,186,565,597 bps INFO @ Sat, 15 Jan 2022 21:57:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05_model.r WARNING @ Sat, 15 Jan 2022 21:57:17: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:57:17: #2 You may need to consider one of the other alternative d(s): 1,138,159,186,565,597 WARNING @ Sat, 15 Jan 2022 21:57:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:57:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:57:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:57:21: 2000000 INFO @ Sat, 15 Jan 2022 21:57:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:57:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:57:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:57:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05_summits.bed INFO @ Sat, 15 Jan 2022 21:57:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (24 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:57:28: 3000000 INFO @ Sat, 15 Jan 2022 21:57:34: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:57:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.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 @ Sat, 15 Jan 2022 21:57:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:57:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:57:41: 5000000 INFO @ Sat, 15 Jan 2022 21:57:45: 1000000 INFO @ Sat, 15 Jan 2022 21:57:47: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:57:47: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:57:47: #1 total tags in treatment: 2462298 INFO @ Sat, 15 Jan 2022 21:57:47: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:57:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:57:47: #1 tags after filtering in treatment: 2224753 INFO @ Sat, 15 Jan 2022 21:57:47: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:57:47: #1 finished! INFO @ Sat, 15 Jan 2022 21:57:47: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:57:47: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 21:57:47: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 21:57:47: start model_add_line... INFO @ Sat, 15 Jan 2022 21:57:47: start X-correlation... INFO @ Sat, 15 Jan 2022 21:57:47: end of X-cor INFO @ Sat, 15 Jan 2022 21:57:47: #2 finished! INFO @ Sat, 15 Jan 2022 21:57:47: #2 predicted fragment length is 159 bps INFO @ Sat, 15 Jan 2022 21:57:47: #2 alternative fragment length(s) may be 1,138,159,186,565,597 bps INFO @ Sat, 15 Jan 2022 21:57:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10_model.r WARNING @ Sat, 15 Jan 2022 21:57:47: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:57:47: #2 You may need to consider one of the other alternative d(s): 1,138,159,186,565,597 WARNING @ Sat, 15 Jan 2022 21:57:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:57:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:57:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:57:51: 2000000 INFO @ Sat, 15 Jan 2022 21:57:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:57:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:57:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:57:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10_summits.bed INFO @ Sat, 15 Jan 2022 21:57:53: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (9 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:57:58: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:58:04: 4000000 INFO @ Sat, 15 Jan 2022 21:58:10: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:58:17: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:58:17: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:58:17: #1 total tags in treatment: 2462298 INFO @ Sat, 15 Jan 2022 21:58:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:58:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:58:17: #1 tags after filtering in treatment: 2224753 INFO @ Sat, 15 Jan 2022 21:58:17: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:58:17: #1 finished! INFO @ Sat, 15 Jan 2022 21:58:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:58:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:58:17: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 21:58:17: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 21:58:17: start model_add_line... INFO @ Sat, 15 Jan 2022 21:58:17: start X-correlation... INFO @ Sat, 15 Jan 2022 21:58:17: end of X-cor INFO @ Sat, 15 Jan 2022 21:58:17: #2 finished! INFO @ Sat, 15 Jan 2022 21:58:17: #2 predicted fragment length is 159 bps INFO @ Sat, 15 Jan 2022 21:58:17: #2 alternative fragment length(s) may be 1,138,159,186,565,597 bps INFO @ Sat, 15 Jan 2022 21:58:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20_model.r WARNING @ Sat, 15 Jan 2022 21:58:17: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:58:17: #2 You may need to consider one of the other alternative d(s): 1,138,159,186,565,597 WARNING @ Sat, 15 Jan 2022 21:58:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:58:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:58:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:58:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20_summits.bed INFO @ Sat, 15 Jan 2022 21:58:23: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 13 millis CompletedMACS2peakCalling