Job ID = 14521780 SRX = ERX4439640 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3838079 spots for ERR4501569/ERR4501569.sra Written 3838079 spots for ERR4501569/ERR4501569.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: 00:03:07 3838079 reads; of these: 3838079 (100.00%) were paired; of these: 1031030 (26.86%) aligned concordantly 0 times 2402983 (62.61%) aligned concordantly exactly 1 time 404066 (10.53%) aligned concordantly >1 times ---- 1031030 pairs aligned concordantly 0 times; of these: 453695 (44.00%) aligned discordantly 1 time ---- 577335 pairs aligned 0 times concordantly or discordantly; of these: 1154670 mates make up the pairs; of these: 925747 (80.17%) aligned 0 times 64698 (5.60%) aligned exactly 1 time 164225 (14.22%) aligned >1 times 87.94% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 56052 / 3229515 = 0.0174 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 21:44:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.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 21:44:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:44:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:44:19: 1000000 INFO @ Sat, 15 Jan 2022 21:44:25: 2000000 INFO @ Sat, 15 Jan 2022 21:44:31: 3000000 INFO @ Sat, 15 Jan 2022 21:44:36: 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 21:44:42: 5000000 INFO @ Sat, 15 Jan 2022 21:44:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.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 21:44:44: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:44:44: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:44:48: 6000000 INFO @ Sat, 15 Jan 2022 21:44:50: 1000000 INFO @ Sat, 15 Jan 2022 21:44:52: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:44:52: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:44:52: #1 total tags in treatment: 2759090 INFO @ Sat, 15 Jan 2022 21:44:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:44:52: #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 21:44:52: #1 tags after filtering in treatment: 2389255 INFO @ Sat, 15 Jan 2022 21:44:52: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:44:52: #1 finished! INFO @ Sat, 15 Jan 2022 21:44:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:44:52: #2 number of paired peaks: 112 WARNING @ Sat, 15 Jan 2022 21:44:52: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 15 Jan 2022 21:44:52: start model_add_line... INFO @ Sat, 15 Jan 2022 21:44:52: start X-correlation... INFO @ Sat, 15 Jan 2022 21:44:52: end of X-cor INFO @ Sat, 15 Jan 2022 21:44:52: #2 finished! INFO @ Sat, 15 Jan 2022 21:44:52: #2 predicted fragment length is 158 bps INFO @ Sat, 15 Jan 2022 21:44:52: #2 alternative fragment length(s) may be 1,158,206,523,556,581 bps INFO @ Sat, 15 Jan 2022 21:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05_model.r WARNING @ Sat, 15 Jan 2022 21:44:52: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:44:52: #2 You may need to consider one of the other alternative d(s): 1,158,206,523,556,581 WARNING @ Sat, 15 Jan 2022 21:44:52: #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 21:44:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:44:55: 2000000 INFO @ Sat, 15 Jan 2022 21:44:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:44:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:44:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:44:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05_summits.bed INFO @ Sat, 15 Jan 2022 21:44:58: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:45:01: 3000000 INFO @ Sat, 15 Jan 2022 21:45:07: 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 21:45:13: 5000000 INFO @ Sat, 15 Jan 2022 21:45:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.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 21:45:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:45:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:45:19: 6000000 INFO @ Sat, 15 Jan 2022 21:45:21: 1000000 INFO @ Sat, 15 Jan 2022 21:45:23: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:45:23: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:45:23: #1 total tags in treatment: 2759090 INFO @ Sat, 15 Jan 2022 21:45:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:45:23: #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 21:45:23: #1 tags after filtering in treatment: 2389255 INFO @ Sat, 15 Jan 2022 21:45:23: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:45:23: #1 finished! INFO @ Sat, 15 Jan 2022 21:45:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:45:24: #2 number of paired peaks: 112 WARNING @ Sat, 15 Jan 2022 21:45:24: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 15 Jan 2022 21:45:24: start model_add_line... INFO @ Sat, 15 Jan 2022 21:45:24: start X-correlation... INFO @ Sat, 15 Jan 2022 21:45:24: end of X-cor INFO @ Sat, 15 Jan 2022 21:45:24: #2 finished! INFO @ Sat, 15 Jan 2022 21:45:24: #2 predicted fragment length is 158 bps INFO @ Sat, 15 Jan 2022 21:45:24: #2 alternative fragment length(s) may be 1,158,206,523,556,581 bps INFO @ Sat, 15 Jan 2022 21:45:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10_model.r WARNING @ Sat, 15 Jan 2022 21:45:24: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:45:24: #2 You may need to consider one of the other alternative d(s): 1,158,206,523,556,581 WARNING @ Sat, 15 Jan 2022 21:45:24: #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 21:45:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:45:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:45:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:45:29: 2000000 INFO @ Sat, 15 Jan 2022 21:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10_summits.bed INFO @ Sat, 15 Jan 2022 21:45:30: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:45:36: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:45:43: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:45:51: 5000000 INFO @ Sat, 15 Jan 2022 21:45:58: 6000000 INFO @ Sat, 15 Jan 2022 21:46:03: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:46:03: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:46:03: #1 total tags in treatment: 2759090 INFO @ Sat, 15 Jan 2022 21:46:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:46:03: #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 21:46:03: #1 tags after filtering in treatment: 2389255 INFO @ Sat, 15 Jan 2022 21:46:03: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:46:03: #1 finished! INFO @ Sat, 15 Jan 2022 21:46:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:46:03: #2 number of paired peaks: 112 WARNING @ Sat, 15 Jan 2022 21:46:03: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 15 Jan 2022 21:46:03: start model_add_line... INFO @ Sat, 15 Jan 2022 21:46:03: start X-correlation... INFO @ Sat, 15 Jan 2022 21:46:03: end of X-cor INFO @ Sat, 15 Jan 2022 21:46:03: #2 finished! INFO @ Sat, 15 Jan 2022 21:46:03: #2 predicted fragment length is 158 bps INFO @ Sat, 15 Jan 2022 21:46:03: #2 alternative fragment length(s) may be 1,158,206,523,556,581 bps INFO @ Sat, 15 Jan 2022 21:46:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20_model.r WARNING @ Sat, 15 Jan 2022 21:46:03: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:46:03: #2 You may need to consider one of the other alternative d(s): 1,158,206,523,556,581 WARNING @ Sat, 15 Jan 2022 21:46:03: #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 21:46:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:46:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:46:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:46:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:46:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:46:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20_summits.bed INFO @ Sat, 15 Jan 2022 21:46:10: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling