Job ID = 12531635 SRX = SRX4555015 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12473834 spots for SRR7696705/SRR7696705.sra Written 12473834 spots for SRR7696705/SRR7696705.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: 00:14:16 12473834 reads; of these: 12473834 (100.00%) were paired; of these: 688652 (5.52%) aligned concordantly 0 times 5748862 (46.09%) aligned concordantly exactly 1 time 6036320 (48.39%) aligned concordantly >1 times ---- 688652 pairs aligned concordantly 0 times; of these: 43857 (6.37%) aligned discordantly 1 time ---- 644795 pairs aligned 0 times concordantly or discordantly; of these: 1289590 mates make up the pairs; of these: 1009536 (78.28%) aligned 0 times 151310 (11.73%) aligned exactly 1 time 128744 (9.98%) aligned >1 times 95.95% overall alignment rate Time searching: 00:14:16 Overall time: 00:14:16 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 16 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] 2605698 / 5787192 = 0.4503 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:08:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.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, 17 Apr 2021 09:08:58: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:08:58: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:09:04: 1000000 INFO @ Sat, 17 Apr 2021 09:09:09: 2000000 INFO @ Sat, 17 Apr 2021 09:09:15: 3000000 INFO @ Sat, 17 Apr 2021 09:09:21: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:09:27: 5000000 INFO @ Sat, 17 Apr 2021 09:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.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, 17 Apr 2021 09:09:28: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:09:28: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:09:33: 6000000 INFO @ Sat, 17 Apr 2021 09:09:35: 1000000 INFO @ Sat, 17 Apr 2021 09:09:39: 7000000 INFO @ Sat, 17 Apr 2021 09:09:42: 2000000 INFO @ Sat, 17 Apr 2021 09:09:45: 8000000 INFO @ Sat, 17 Apr 2021 09:09:50: 3000000 INFO @ Sat, 17 Apr 2021 09:09:50: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:09:56: 10000000 INFO @ Sat, 17 Apr 2021 09:09:57: 4000000 INFO @ Sat, 17 Apr 2021 09:09:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.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, 17 Apr 2021 09:09:58: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:09:58: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:10:02: 11000000 INFO @ Sat, 17 Apr 2021 09:10:04: 1000000 INFO @ Sat, 17 Apr 2021 09:10:04: 5000000 INFO @ Sat, 17 Apr 2021 09:10:08: 12000000 INFO @ Sat, 17 Apr 2021 09:10:10: 2000000 INFO @ Sat, 17 Apr 2021 09:10:11: 6000000 INFO @ Sat, 17 Apr 2021 09:10:13: 13000000 INFO @ Sat, 17 Apr 2021 09:10:16: 3000000 INFO @ Sat, 17 Apr 2021 09:10:18: 7000000 INFO @ Sat, 17 Apr 2021 09:10:19: 14000000 INFO @ Sat, 17 Apr 2021 09:10:23: 4000000 INFO @ Sat, 17 Apr 2021 09:10:25: 15000000 INFO @ Sat, 17 Apr 2021 09:10:25: 8000000 INFO @ Sat, 17 Apr 2021 09:10:29: 5000000 INFO @ Sat, 17 Apr 2021 09:10:31: 16000000 INFO @ Sat, 17 Apr 2021 09:10:32: 9000000 INFO @ Sat, 17 Apr 2021 09:10:35: 6000000 INFO @ Sat, 17 Apr 2021 09:10:37: 17000000 INFO @ Sat, 17 Apr 2021 09:10:39: 10000000 INFO @ Sat, 17 Apr 2021 09:10:41: 7000000 INFO @ Sat, 17 Apr 2021 09:10:44: 18000000 INFO @ Sat, 17 Apr 2021 09:10:46: 11000000 INFO @ Sat, 17 Apr 2021 09:10:47: 8000000 INFO @ Sat, 17 Apr 2021 09:10:48: #1 tag size is determined as 84 bps INFO @ Sat, 17 Apr 2021 09:10:48: #1 tag size = 84 INFO @ Sat, 17 Apr 2021 09:10:48: #1 total tags in treatment: 9182467 INFO @ Sat, 17 Apr 2021 09:10:48: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:10:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:10:48: #1 tags after filtering in treatment: 2224737 INFO @ Sat, 17 Apr 2021 09:10:48: #1 Redundant rate of treatment: 0.76 INFO @ Sat, 17 Apr 2021 09:10:48: #1 finished! INFO @ Sat, 17 Apr 2021 09:10:48: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:10:49: #2 number of paired peaks: 133 WARNING @ Sat, 17 Apr 2021 09:10:49: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 17 Apr 2021 09:10:49: start model_add_line... INFO @ Sat, 17 Apr 2021 09:10:49: start X-correlation... INFO @ Sat, 17 Apr 2021 09:10:49: end of X-cor INFO @ Sat, 17 Apr 2021 09:10:49: #2 finished! INFO @ Sat, 17 Apr 2021 09:10:49: #2 predicted fragment length is 3 bps INFO @ Sat, 17 Apr 2021 09:10:49: #2 alternative fragment length(s) may be 3,593,596 bps INFO @ Sat, 17 Apr 2021 09:10:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.05_model.r WARNING @ Sat, 17 Apr 2021 09:10:49: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:10:49: #2 You may need to consider one of the other alternative d(s): 3,593,596 WARNING @ Sat, 17 Apr 2021 09:10:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:10:49: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:10:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:10:52: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:10:53: 12000000 INFO @ Sat, 17 Apr 2021 09:10:53: 9000000 INFO @ Sat, 17 Apr 2021 09:10:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:10:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.05_summits.bed INFO @ Sat, 17 Apr 2021 09:10:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:10:58: 10000000 INFO @ Sat, 17 Apr 2021 09:10:59: 13000000 INFO @ Sat, 17 Apr 2021 09:11:04: 11000000 INFO @ Sat, 17 Apr 2021 09:11:06: 14000000 INFO @ Sat, 17 Apr 2021 09:11:10: 12000000 INFO @ Sat, 17 Apr 2021 09:11:13: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:11:16: 13000000 INFO @ Sat, 17 Apr 2021 09:11:20: 16000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:11:21: 14000000 INFO @ Sat, 17 Apr 2021 09:11:27: 17000000 INFO @ Sat, 17 Apr 2021 09:11:27: 15000000 INFO @ Sat, 17 Apr 2021 09:11:33: 16000000 INFO @ Sat, 17 Apr 2021 09:11:34: 18000000 INFO @ Sat, 17 Apr 2021 09:11:40: 17000000 INFO @ Sat, 17 Apr 2021 09:11:40: #1 tag size is determined as 84 bps INFO @ Sat, 17 Apr 2021 09:11:40: #1 tag size = 84 INFO @ Sat, 17 Apr 2021 09:11:40: #1 total tags in treatment: 9182467 INFO @ Sat, 17 Apr 2021 09:11:40: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:11:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:11:40: #1 tags after filtering in treatment: 2224737 INFO @ Sat, 17 Apr 2021 09:11:40: #1 Redundant rate of treatment: 0.76 INFO @ Sat, 17 Apr 2021 09:11:40: #1 finished! INFO @ Sat, 17 Apr 2021 09:11:40: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:11:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:11:40: #2 number of paired peaks: 133 WARNING @ Sat, 17 Apr 2021 09:11:40: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 17 Apr 2021 09:11:40: start model_add_line... INFO @ Sat, 17 Apr 2021 09:11:40: start X-correlation... INFO @ Sat, 17 Apr 2021 09:11:40: end of X-cor INFO @ Sat, 17 Apr 2021 09:11:40: #2 finished! INFO @ Sat, 17 Apr 2021 09:11:40: #2 predicted fragment length is 3 bps INFO @ Sat, 17 Apr 2021 09:11:40: #2 alternative fragment length(s) may be 3,593,596 bps INFO @ Sat, 17 Apr 2021 09:11:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.10_model.r WARNING @ Sat, 17 Apr 2021 09:11:40: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:11:40: #2 You may need to consider one of the other alternative d(s): 3,593,596 WARNING @ Sat, 17 Apr 2021 09:11:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:11:40: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:11:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:11:44: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:11:46: 18000000 INFO @ Sat, 17 Apr 2021 09:11:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:11:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:11:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.10_summits.bed INFO @ Sat, 17 Apr 2021 09:11:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:11:50: #1 tag size is determined as 84 bps INFO @ Sat, 17 Apr 2021 09:11:50: #1 tag size = 84 INFO @ Sat, 17 Apr 2021 09:11:50: #1 total tags in treatment: 9182467 INFO @ Sat, 17 Apr 2021 09:11:50: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:11:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:11:50: #1 tags after filtering in treatment: 2224737 INFO @ Sat, 17 Apr 2021 09:11:50: #1 Redundant rate of treatment: 0.76 INFO @ Sat, 17 Apr 2021 09:11:50: #1 finished! INFO @ Sat, 17 Apr 2021 09:11:50: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:11:51: #2 number of paired peaks: 133 WARNING @ Sat, 17 Apr 2021 09:11:51: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 17 Apr 2021 09:11:51: start model_add_line... INFO @ Sat, 17 Apr 2021 09:11:51: start X-correlation... INFO @ Sat, 17 Apr 2021 09:11:51: end of X-cor INFO @ Sat, 17 Apr 2021 09:11:51: #2 finished! INFO @ Sat, 17 Apr 2021 09:11:51: #2 predicted fragment length is 3 bps INFO @ Sat, 17 Apr 2021 09:11:51: #2 alternative fragment length(s) may be 3,593,596 bps INFO @ Sat, 17 Apr 2021 09:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.20_model.r WARNING @ Sat, 17 Apr 2021 09:11:51: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:11:51: #2 You may need to consider one of the other alternative d(s): 3,593,596 WARNING @ Sat, 17 Apr 2021 09:11:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:11:51: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:11:54: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:11:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555015/SRX4555015.20_summits.bed INFO @ Sat, 17 Apr 2021 09:11:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling