Job ID = 14521229 SRX = SRX8245384 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9071859 spots for SRR11684595/SRR11684595.sra Written 9071859 spots for SRR11684595/SRR11684595.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: 00:04:14 9071859 reads; of these: 9071859 (100.00%) were paired; of these: 5355083 (59.03%) aligned concordantly 0 times 3413710 (37.63%) aligned concordantly exactly 1 time 303066 (3.34%) aligned concordantly >1 times ---- 5355083 pairs aligned concordantly 0 times; of these: 18456 (0.34%) aligned discordantly 1 time ---- 5336627 pairs aligned 0 times concordantly or discordantly; of these: 10673254 mates make up the pairs; of these: 7004777 (65.63%) aligned 0 times 3293226 (30.85%) aligned exactly 1 time 375251 (3.52%) aligned >1 times 61.39% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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_sort_core] merging from 8 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 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] 296053 / 3734597 = 0.0793 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 20:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.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 20:50:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:50:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:50:20: 1000000 INFO @ Sat, 15 Jan 2022 20:50:25: 2000000 INFO @ Sat, 15 Jan 2022 20:50:30: 3000000 INFO @ Sat, 15 Jan 2022 20:50:35: 4000000 INFO @ Sat, 15 Jan 2022 20:50:40: 5000000 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 20:50:45: 6000000 INFO @ Sat, 15 Jan 2022 20:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.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 20:50:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:50:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:50:50: 7000000 INFO @ Sat, 15 Jan 2022 20:50:51: 1000000 INFO @ Sat, 15 Jan 2022 20:50:56: 8000000 INFO @ Sat, 15 Jan 2022 20:50:56: 2000000 INFO @ Sat, 15 Jan 2022 20:51:01: 9000000 INFO @ Sat, 15 Jan 2022 20:51:02: 3000000 INFO @ Sat, 15 Jan 2022 20:51:07: 10000000 INFO @ Sat, 15 Jan 2022 20:51:07: 4000000 INFO @ Sat, 15 Jan 2022 20:51:10: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:51:10: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:51:10: #1 total tags in treatment: 3421715 INFO @ Sat, 15 Jan 2022 20:51:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:51:10: #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 20:51:10: #1 tags after filtering in treatment: 2170689 INFO @ Sat, 15 Jan 2022 20:51:10: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:51:10: #1 finished! INFO @ Sat, 15 Jan 2022 20:51:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:51:10: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:51:10: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:51:10: start model_add_line... INFO @ Sat, 15 Jan 2022 20:51:10: start X-correlation... INFO @ Sat, 15 Jan 2022 20:51:10: end of X-cor INFO @ Sat, 15 Jan 2022 20:51:10: #2 finished! INFO @ Sat, 15 Jan 2022 20:51:10: #2 predicted fragment length is 49 bps INFO @ Sat, 15 Jan 2022 20:51:10: #2 alternative fragment length(s) may be 23,49,101,119,163,191,209,257,274,289,309,358,375,395,424,464,484,532,554,582 bps INFO @ Sat, 15 Jan 2022 20:51:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.05_model.r WARNING @ Sat, 15 Jan 2022 20:51:10: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:51:10: #2 You may need to consider one of the other alternative d(s): 23,49,101,119,163,191,209,257,274,289,309,358,375,395,424,464,484,532,554,582 WARNING @ Sat, 15 Jan 2022 20:51:10: #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 20:51:10: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:51:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:51:12: 5000000 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 20:51:14: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:51:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.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 20:51:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:51:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:51:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:51:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.05_summits.bed INFO @ Sat, 15 Jan 2022 20:51:15: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:51:17: 6000000 INFO @ Sat, 15 Jan 2022 20:51:20: 1000000 INFO @ Sat, 15 Jan 2022 20:51:23: 7000000 INFO @ Sat, 15 Jan 2022 20:51:26: 2000000 INFO @ Sat, 15 Jan 2022 20:51:28: 8000000 INFO @ Sat, 15 Jan 2022 20:51:31: 3000000 INFO @ Sat, 15 Jan 2022 20:51:34: 9000000 INFO @ Sat, 15 Jan 2022 20:51:36: 4000000 INFO @ Sat, 15 Jan 2022 20:51:39: 10000000 INFO @ Sat, 15 Jan 2022 20:51:42: 5000000 INFO @ Sat, 15 Jan 2022 20:51:42: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:51:42: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:51:42: #1 total tags in treatment: 3421715 INFO @ Sat, 15 Jan 2022 20:51:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:51:42: #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 20:51:42: #1 tags after filtering in treatment: 2170689 INFO @ Sat, 15 Jan 2022 20:51:42: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:51:42: #1 finished! INFO @ Sat, 15 Jan 2022 20:51:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:51:42: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:51:42: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:51:42: start model_add_line... INFO @ Sat, 15 Jan 2022 20:51:42: start X-correlation... INFO @ Sat, 15 Jan 2022 20:51:42: end of X-cor INFO @ Sat, 15 Jan 2022 20:51:42: #2 finished! INFO @ Sat, 15 Jan 2022 20:51:42: #2 predicted fragment length is 49 bps INFO @ Sat, 15 Jan 2022 20:51:42: #2 alternative fragment length(s) may be 23,49,101,119,163,191,209,257,274,289,309,358,375,395,424,464,484,532,554,582 bps INFO @ Sat, 15 Jan 2022 20:51:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.10_model.r WARNING @ Sat, 15 Jan 2022 20:51:42: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:51:42: #2 You may need to consider one of the other alternative d(s): 23,49,101,119,163,191,209,257,274,289,309,358,375,395,424,464,484,532,554,582 WARNING @ Sat, 15 Jan 2022 20:51:42: #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 20:51:42: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:51:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:51:47: 6000000 INFO @ Sat, 15 Jan 2022 20:51:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:51:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:51:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.10_summits.bed INFO @ Sat, 15 Jan 2022 20:51:47: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (34 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:51:52: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:51:57: 8000000 INFO @ Sat, 15 Jan 2022 20:52:02: 9000000 INFO @ Sat, 15 Jan 2022 20:52:06: 10000000 INFO @ Sat, 15 Jan 2022 20:52:09: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:52:09: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:52:09: #1 total tags in treatment: 3421715 INFO @ Sat, 15 Jan 2022 20:52:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:09: #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 20:52:09: #1 tags after filtering in treatment: 2170689 INFO @ Sat, 15 Jan 2022 20:52:09: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:52:09: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:09: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:52:09: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:09: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:09: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:09: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:09: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:09: #2 predicted fragment length is 49 bps INFO @ Sat, 15 Jan 2022 20:52:09: #2 alternative fragment length(s) may be 23,49,101,119,163,191,209,257,274,289,309,358,375,395,424,464,484,532,554,582 bps INFO @ Sat, 15 Jan 2022 20:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.20_model.r WARNING @ Sat, 15 Jan 2022 20:52:09: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:52:09: #2 You may need to consider one of the other alternative d(s): 23,49,101,119,163,191,209,257,274,289,309,358,375,395,424,464,484,532,554,582 WARNING @ Sat, 15 Jan 2022 20:52:09: #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 20:52:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:13: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245384/SRX8245384.20_summits.bed INFO @ Sat, 15 Jan 2022 20:52:14: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling