Job ID = 12531633 SRX = SRX4555014 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16298797 spots for SRR7696704/SRR7696704.sra Written 16298797 spots for SRR7696704/SRR7696704.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: 00:17:28 16298797 reads; of these: 16298797 (100.00%) were paired; of these: 926348 (5.68%) aligned concordantly 0 times 7529926 (46.20%) aligned concordantly exactly 1 time 7842523 (48.12%) aligned concordantly >1 times ---- 926348 pairs aligned concordantly 0 times; of these: 61524 (6.64%) aligned discordantly 1 time ---- 864824 pairs aligned 0 times concordantly or discordantly; of these: 1729648 mates make up the pairs; of these: 1313014 (75.91%) aligned 0 times 223056 (12.90%) aligned exactly 1 time 193578 (11.19%) aligned >1 times 95.97% overall alignment rate Time searching: 00:17:28 Overall time: 00:17:28 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 24 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] 3350118 / 7076034 = 0.4734 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 09:13:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.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 09:13:27: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:13:27: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:13:35: 1000000 INFO @ Sat, 17 Apr 2021 09:13:42: 2000000 INFO @ Sat, 17 Apr 2021 09:13:50: 3000000 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 09:13:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.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 09:13:57: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:13:57: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:13:57: 4000000 INFO @ Sat, 17 Apr 2021 09:14:07: 5000000 INFO @ Sat, 17 Apr 2021 09:14:07: 1000000 INFO @ Sat, 17 Apr 2021 09:14:16: 6000000 INFO @ Sat, 17 Apr 2021 09:14:18: 2000000 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 09:14:26: 7000000 INFO @ Sat, 17 Apr 2021 09:14:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.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 09:14:27: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:14:27: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:14:28: 3000000 INFO @ Sat, 17 Apr 2021 09:14:36: 8000000 INFO @ Sat, 17 Apr 2021 09:14:37: 1000000 INFO @ Sat, 17 Apr 2021 09:14:39: 4000000 INFO @ Sat, 17 Apr 2021 09:14:46: 9000000 INFO @ Sat, 17 Apr 2021 09:14:47: 2000000 INFO @ Sat, 17 Apr 2021 09:14:49: 5000000 INFO @ Sat, 17 Apr 2021 09:14:55: 10000000 INFO @ Sat, 17 Apr 2021 09:14:57: 3000000 INFO @ Sat, 17 Apr 2021 09:14:59: 6000000 INFO @ Sat, 17 Apr 2021 09:15:04: 11000000 INFO @ Sat, 17 Apr 2021 09:15:06: 4000000 INFO @ Sat, 17 Apr 2021 09:15:09: 7000000 INFO @ Sat, 17 Apr 2021 09:15:14: 12000000 INFO @ Sat, 17 Apr 2021 09:15:16: 5000000 INFO @ Sat, 17 Apr 2021 09:15:20: 8000000 INFO @ Sat, 17 Apr 2021 09:15:23: 13000000 INFO @ Sat, 17 Apr 2021 09:15:26: 6000000 INFO @ Sat, 17 Apr 2021 09:15:30: 9000000 INFO @ Sat, 17 Apr 2021 09:15:32: 14000000 INFO @ Sat, 17 Apr 2021 09:15:36: 7000000 INFO @ Sat, 17 Apr 2021 09:15:41: 10000000 INFO @ Sat, 17 Apr 2021 09:15:41: 15000000 INFO @ Sat, 17 Apr 2021 09:15:45: 8000000 INFO @ Sat, 17 Apr 2021 09:15:50: 11000000 INFO @ Sat, 17 Apr 2021 09:15:51: 16000000 INFO @ Sat, 17 Apr 2021 09:15:55: 9000000 INFO @ Sat, 17 Apr 2021 09:16:00: 17000000 INFO @ Sat, 17 Apr 2021 09:16:00: 12000000 INFO @ Sat, 17 Apr 2021 09:16:05: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:16:09: 18000000 INFO @ Sat, 17 Apr 2021 09:16:10: 13000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:16:14: 11000000 INFO @ Sat, 17 Apr 2021 09:16:18: 19000000 INFO @ Sat, 17 Apr 2021 09:16:20: 14000000 INFO @ Sat, 17 Apr 2021 09:16:23: 12000000 INFO @ Sat, 17 Apr 2021 09:16:28: 20000000 INFO @ Sat, 17 Apr 2021 09:16:30: 15000000 INFO @ Sat, 17 Apr 2021 09:16:32: 13000000 INFO @ Sat, 17 Apr 2021 09:16:38: 21000000 INFO @ Sat, 17 Apr 2021 09:16:39: 16000000 INFO @ Sat, 17 Apr 2021 09:16:42: 14000000 INFO @ Sat, 17 Apr 2021 09:16:47: 22000000 INFO @ Sat, 17 Apr 2021 09:16:49: 17000000 INFO @ Sat, 17 Apr 2021 09:16:51: 15000000 INFO @ Sat, 17 Apr 2021 09:16:57: 23000000 INFO @ Sat, 17 Apr 2021 09:16:58: 18000000 INFO @ Sat, 17 Apr 2021 09:17:00: 16000000 INFO @ Sat, 17 Apr 2021 09:17:06: 24000000 INFO @ Sat, 17 Apr 2021 09:17:08: 19000000 INFO @ Sat, 17 Apr 2021 09:17:09: 17000000 INFO @ Sat, 17 Apr 2021 09:17:12: #1 tag size is determined as 78 bps INFO @ Sat, 17 Apr 2021 09:17:12: #1 tag size = 78 INFO @ Sat, 17 Apr 2021 09:17:12: #1 total tags in treatment: 12026991 INFO @ Sat, 17 Apr 2021 09:17:12: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:17:12: #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 09:17:12: #1 tags after filtering in treatment: 2591474 INFO @ Sat, 17 Apr 2021 09:17:12: #1 Redundant rate of treatment: 0.78 INFO @ Sat, 17 Apr 2021 09:17:12: #1 finished! INFO @ Sat, 17 Apr 2021 09:17:12: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:17:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:17:13: #2 number of paired peaks: 103 WARNING @ Sat, 17 Apr 2021 09:17:13: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Sat, 17 Apr 2021 09:17:13: start model_add_line... INFO @ Sat, 17 Apr 2021 09:17:13: start X-correlation... INFO @ Sat, 17 Apr 2021 09:17:13: end of X-cor INFO @ Sat, 17 Apr 2021 09:17:13: #2 finished! INFO @ Sat, 17 Apr 2021 09:17:13: #2 predicted fragment length is 3 bps INFO @ Sat, 17 Apr 2021 09:17:13: #2 alternative fragment length(s) may be 3,597 bps INFO @ Sat, 17 Apr 2021 09:17:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.05_model.r WARNING @ Sat, 17 Apr 2021 09:17:13: #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 09:17:13: #2 You may need to consider one of the other alternative d(s): 3,597 WARNING @ Sat, 17 Apr 2021 09:17:13: #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 09:17:13: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:17:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:17:17: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:17:18: 20000000 INFO @ Sat, 17 Apr 2021 09:17:18: 18000000 INFO @ Sat, 17 Apr 2021 09:17:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:17:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:17:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.05_summits.bed INFO @ Sat, 17 Apr 2021 09:17:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:17:27: 19000000 INFO @ Sat, 17 Apr 2021 09:17:28: 21000000 INFO @ Sat, 17 Apr 2021 09:17:36: 20000000 INFO @ Sat, 17 Apr 2021 09:17:38: 22000000 INFO @ Sat, 17 Apr 2021 09:17:46: 21000000 INFO @ Sat, 17 Apr 2021 09:17:48: 23000000 INFO @ Sat, 17 Apr 2021 09:17:56: 22000000 INFO @ Sat, 17 Apr 2021 09:17:58: 24000000 INFO @ Sat, 17 Apr 2021 09:18:04: #1 tag size is determined as 78 bps INFO @ Sat, 17 Apr 2021 09:18:04: #1 tag size = 78 INFO @ Sat, 17 Apr 2021 09:18:04: #1 total tags in treatment: 12026991 INFO @ Sat, 17 Apr 2021 09:18:04: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:18:04: #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 09:18:04: #1 tags after filtering in treatment: 2591474 INFO @ Sat, 17 Apr 2021 09:18:04: #1 Redundant rate of treatment: 0.78 INFO @ Sat, 17 Apr 2021 09:18:04: #1 finished! INFO @ Sat, 17 Apr 2021 09:18:04: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:18:05: #2 number of paired peaks: 103 WARNING @ Sat, 17 Apr 2021 09:18:05: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Sat, 17 Apr 2021 09:18:05: start model_add_line... INFO @ Sat, 17 Apr 2021 09:18:05: start X-correlation... INFO @ Sat, 17 Apr 2021 09:18:05: end of X-cor INFO @ Sat, 17 Apr 2021 09:18:05: #2 finished! INFO @ Sat, 17 Apr 2021 09:18:05: #2 predicted fragment length is 3 bps INFO @ Sat, 17 Apr 2021 09:18:05: #2 alternative fragment length(s) may be 3,597 bps INFO @ Sat, 17 Apr 2021 09:18:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.10_model.r WARNING @ Sat, 17 Apr 2021 09:18:05: #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 09:18:05: #2 You may need to consider one of the other alternative d(s): 3,597 WARNING @ Sat, 17 Apr 2021 09:18:05: #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 09:18:05: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:18:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:18:05: 23000000 INFO @ Sat, 17 Apr 2021 09:18:09: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:18:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:18:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:18:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.10_summits.bed INFO @ Sat, 17 Apr 2021 09:18:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:18:14: 24000000 INFO @ Sat, 17 Apr 2021 09:18:18: #1 tag size is determined as 78 bps INFO @ Sat, 17 Apr 2021 09:18:18: #1 tag size = 78 INFO @ Sat, 17 Apr 2021 09:18:18: #1 total tags in treatment: 12026991 INFO @ Sat, 17 Apr 2021 09:18:18: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:18:18: #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 09:18:19: #1 tags after filtering in treatment: 2591474 INFO @ Sat, 17 Apr 2021 09:18:19: #1 Redundant rate of treatment: 0.78 INFO @ Sat, 17 Apr 2021 09:18:19: #1 finished! INFO @ Sat, 17 Apr 2021 09:18:19: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:18:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:18:19: #2 number of paired peaks: 103 WARNING @ Sat, 17 Apr 2021 09:18:19: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Sat, 17 Apr 2021 09:18:19: start model_add_line... INFO @ Sat, 17 Apr 2021 09:18:19: start X-correlation... INFO @ Sat, 17 Apr 2021 09:18:19: end of X-cor INFO @ Sat, 17 Apr 2021 09:18:19: #2 finished! INFO @ Sat, 17 Apr 2021 09:18:19: #2 predicted fragment length is 3 bps INFO @ Sat, 17 Apr 2021 09:18:19: #2 alternative fragment length(s) may be 3,597 bps INFO @ Sat, 17 Apr 2021 09:18:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.20_model.r WARNING @ Sat, 17 Apr 2021 09:18:19: #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 09:18:19: #2 You may need to consider one of the other alternative d(s): 3,597 WARNING @ Sat, 17 Apr 2021 09:18:19: #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 09:18:19: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:18:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:18:23: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:18:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:18:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:18:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555014/SRX4555014.20_summits.bed INFO @ Sat, 17 Apr 2021 09:18:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling