Job ID = 12531671 SRX = SRX4555043 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13903687 spots for SRR7696740/SRR7696740.sra Written 13903687 spots for SRR7696740/SRR7696740.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: 00:15:47 13903687 reads; of these: 13903687 (100.00%) were paired; of these: 813222 (5.85%) aligned concordantly 0 times 6150936 (44.24%) aligned concordantly exactly 1 time 6939529 (49.91%) aligned concordantly >1 times ---- 813222 pairs aligned concordantly 0 times; of these: 49656 (6.11%) aligned discordantly 1 time ---- 763566 pairs aligned 0 times concordantly or discordantly; of these: 1527132 mates make up the pairs; of these: 1181061 (77.34%) aligned 0 times 187594 (12.28%) aligned exactly 1 time 158477 (10.38%) aligned >1 times 95.75% overall alignment rate Time searching: 00:15:47 Overall time: 00:15:47 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 20 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] 2652524 / 5858116 = 0.4528 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 09:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.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 09:28:02: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:28:02: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:28:09: 1000000 INFO @ Sat, 17 Apr 2021 09:28:16: 2000000 INFO @ Sat, 17 Apr 2021 09:28:23: 3000000 INFO @ Sat, 17 Apr 2021 09:28:29: 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 09:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.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 09:28:32: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:28:32: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:28:37: 5000000 INFO @ Sat, 17 Apr 2021 09:28:41: 1000000 INFO @ Sat, 17 Apr 2021 09:28:45: 6000000 INFO @ Sat, 17 Apr 2021 09:28:51: 2000000 INFO @ Sat, 17 Apr 2021 09:28:53: 7000000 INFO @ Sat, 17 Apr 2021 09:28:59: 3000000 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 09:29:00: 8000000 INFO @ Sat, 17 Apr 2021 09:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.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 09:29:02: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:29:02: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:29:08: 9000000 INFO @ Sat, 17 Apr 2021 09:29:08: 4000000 INFO @ Sat, 17 Apr 2021 09:29:10: 1000000 INFO @ Sat, 17 Apr 2021 09:29:15: 10000000 INFO @ Sat, 17 Apr 2021 09:29:17: 5000000 INFO @ Sat, 17 Apr 2021 09:29:18: 2000000 INFO @ Sat, 17 Apr 2021 09:29:23: 11000000 INFO @ Sat, 17 Apr 2021 09:29:26: 6000000 INFO @ Sat, 17 Apr 2021 09:29:27: 3000000 INFO @ Sat, 17 Apr 2021 09:29:30: 12000000 INFO @ Sat, 17 Apr 2021 09:29:35: 4000000 INFO @ Sat, 17 Apr 2021 09:29:35: 7000000 INFO @ Sat, 17 Apr 2021 09:29:38: 13000000 INFO @ Sat, 17 Apr 2021 09:29:43: 5000000 INFO @ Sat, 17 Apr 2021 09:29:44: 8000000 INFO @ Sat, 17 Apr 2021 09:29:45: 14000000 INFO @ Sat, 17 Apr 2021 09:29:51: 6000000 INFO @ Sat, 17 Apr 2021 09:29:53: 9000000 INFO @ Sat, 17 Apr 2021 09:29:53: 15000000 INFO @ Sat, 17 Apr 2021 09:29:59: 7000000 INFO @ Sat, 17 Apr 2021 09:30:00: 16000000 INFO @ Sat, 17 Apr 2021 09:30:01: 10000000 INFO @ Sat, 17 Apr 2021 09:30:07: 8000000 INFO @ Sat, 17 Apr 2021 09:30:08: 17000000 INFO @ Sat, 17 Apr 2021 09:30:10: 11000000 INFO @ Sat, 17 Apr 2021 09:30:15: 9000000 INFO @ Sat, 17 Apr 2021 09:30:16: 18000000 INFO @ Sat, 17 Apr 2021 09:30:18: 12000000 INFO @ Sat, 17 Apr 2021 09:30:23: 10000000 INFO @ Sat, 17 Apr 2021 09:30:24: 19000000 INFO @ Sat, 17 Apr 2021 09:30:27: 13000000 INFO @ Sat, 17 Apr 2021 09:30:30: 11000000 INFO @ Sat, 17 Apr 2021 09:30:33: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:30:36: 14000000 INFO @ Sat, 17 Apr 2021 09:30:38: 12000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:30:41: 21000000 INFO @ Sat, 17 Apr 2021 09:30:44: #1 tag size is determined as 75 bps INFO @ Sat, 17 Apr 2021 09:30:44: #1 tag size = 75 INFO @ Sat, 17 Apr 2021 09:30:44: #1 total tags in treatment: 10442002 INFO @ Sat, 17 Apr 2021 09:30:44: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:30:44: #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 09:30:44: #1 tags after filtering in treatment: 2395027 INFO @ Sat, 17 Apr 2021 09:30:44: #1 Redundant rate of treatment: 0.77 INFO @ Sat, 17 Apr 2021 09:30:44: #1 finished! INFO @ Sat, 17 Apr 2021 09:30:44: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:30:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:30:44: #2 number of paired peaks: 128 WARNING @ Sat, 17 Apr 2021 09:30:44: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 17 Apr 2021 09:30:44: start model_add_line... INFO @ Sat, 17 Apr 2021 09:30:44: start X-correlation... INFO @ Sat, 17 Apr 2021 09:30:44: end of X-cor INFO @ Sat, 17 Apr 2021 09:30:44: #2 finished! INFO @ Sat, 17 Apr 2021 09:30:44: #2 predicted fragment length is 3 bps INFO @ Sat, 17 Apr 2021 09:30:44: #2 alternative fragment length(s) may be 3 bps INFO @ Sat, 17 Apr 2021 09:30:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.05_model.r WARNING @ Sat, 17 Apr 2021 09:30:44: #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 09:30:44: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sat, 17 Apr 2021 09:30:44: #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 09:30:44: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:30:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:30:44: 15000000 INFO @ Sat, 17 Apr 2021 09:30:46: 13000000 INFO @ Sat, 17 Apr 2021 09:30:48: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:30:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:30:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:30:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.05_summits.bed INFO @ Sat, 17 Apr 2021 09:30:50: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:30:53: 16000000 INFO @ Sat, 17 Apr 2021 09:30:53: 14000000 INFO @ Sat, 17 Apr 2021 09:31:01: 15000000 INFO @ Sat, 17 Apr 2021 09:31:01: 17000000 INFO @ Sat, 17 Apr 2021 09:31:09: 16000000 INFO @ Sat, 17 Apr 2021 09:31:10: 18000000 INFO @ Sat, 17 Apr 2021 09:31:16: 17000000 INFO @ Sat, 17 Apr 2021 09:31:19: 19000000 INFO @ Sat, 17 Apr 2021 09:31:24: 18000000 INFO @ Sat, 17 Apr 2021 09:31:28: 20000000 INFO @ Sat, 17 Apr 2021 09:31:32: 19000000 INFO @ Sat, 17 Apr 2021 09:31:37: 21000000 INFO @ Sat, 17 Apr 2021 09:31:40: #1 tag size is determined as 75 bps INFO @ Sat, 17 Apr 2021 09:31:40: #1 tag size = 75 INFO @ Sat, 17 Apr 2021 09:31:40: #1 total tags in treatment: 10442002 INFO @ Sat, 17 Apr 2021 09:31:40: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:31:40: #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 09:31:40: #1 tags after filtering in treatment: 2395027 INFO @ Sat, 17 Apr 2021 09:31:40: #1 Redundant rate of treatment: 0.77 INFO @ Sat, 17 Apr 2021 09:31:40: #1 finished! INFO @ Sat, 17 Apr 2021 09:31:40: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:31:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:31:41: #2 number of paired peaks: 128 WARNING @ Sat, 17 Apr 2021 09:31:41: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 17 Apr 2021 09:31:41: start model_add_line... INFO @ Sat, 17 Apr 2021 09:31:41: start X-correlation... INFO @ Sat, 17 Apr 2021 09:31:41: 20000000 INFO @ Sat, 17 Apr 2021 09:31:41: end of X-cor INFO @ Sat, 17 Apr 2021 09:31:41: #2 finished! INFO @ Sat, 17 Apr 2021 09:31:41: #2 predicted fragment length is 3 bps INFO @ Sat, 17 Apr 2021 09:31:41: #2 alternative fragment length(s) may be 3 bps INFO @ Sat, 17 Apr 2021 09:31:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.10_model.r WARNING @ Sat, 17 Apr 2021 09:31:41: #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 09:31:41: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sat, 17 Apr 2021 09:31:41: #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 09:31:41: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:31:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:31:45: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:31:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:31:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:31:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.10_summits.bed INFO @ Sat, 17 Apr 2021 09:31:47: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:31:48: 21000000 INFO @ Sat, 17 Apr 2021 09:31:50: #1 tag size is determined as 75 bps INFO @ Sat, 17 Apr 2021 09:31:50: #1 tag size = 75 INFO @ Sat, 17 Apr 2021 09:31:50: #1 total tags in treatment: 10442002 INFO @ Sat, 17 Apr 2021 09:31:50: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:31:50: #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 09:31:50: #1 tags after filtering in treatment: 2395027 INFO @ Sat, 17 Apr 2021 09:31:50: #1 Redundant rate of treatment: 0.77 INFO @ Sat, 17 Apr 2021 09:31:50: #1 finished! INFO @ Sat, 17 Apr 2021 09:31:50: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:31:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:31:51: #2 number of paired peaks: 128 WARNING @ Sat, 17 Apr 2021 09:31:51: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 17 Apr 2021 09:31:51: start model_add_line... INFO @ Sat, 17 Apr 2021 09:31:51: start X-correlation... INFO @ Sat, 17 Apr 2021 09:31:51: end of X-cor INFO @ Sat, 17 Apr 2021 09:31:51: #2 finished! INFO @ Sat, 17 Apr 2021 09:31:51: #2 predicted fragment length is 3 bps INFO @ Sat, 17 Apr 2021 09:31:51: #2 alternative fragment length(s) may be 3 bps INFO @ Sat, 17 Apr 2021 09:31:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.20_model.r WARNING @ Sat, 17 Apr 2021 09:31:51: #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 09:31:51: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sat, 17 Apr 2021 09:31:51: #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 09:31:51: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:31:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:31:55: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:31:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:31:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:31:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555043/SRX4555043.20_summits.bed INFO @ Sat, 17 Apr 2021 09:31:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling