Job ID = 10223781 SRX = ERX4439560 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:02:00 prefetch.2.10.7: 1) Downloading 'ERR4501489'... 2020-10-15T23:02:00 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:02:44 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:02:44 prefetch.2.10.7: 'ERR4501489' is valid 2020-10-15T23:02:44 prefetch.2.10.7: 1) 'ERR4501489' was downloaded successfully 2020-10-15T23:03:12 prefetch.2.10.7: 'ERR4501489' has 5 unresolved dependencies 2020-10-15T23:03:12 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:03:12 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:03:24 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:03:24 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:03:24 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:03:24 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:03:36 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:03:36 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:03:36 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:03:36 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:03:48 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:03:48 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:03:48 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:03:48 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:04:00 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:04:00 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:04:00 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:04:00 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:04:06 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:04:06 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3441521 spots for ERR4501489/ERR4501489.sra Written 3441521 spots for ERR4501489/ERR4501489.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: 00:02:38 3441521 reads; of these: 3441521 (100.00%) were paired; of these: 843387 (24.51%) aligned concordantly 0 times 2096368 (60.91%) aligned concordantly exactly 1 time 501766 (14.58%) aligned concordantly >1 times ---- 843387 pairs aligned concordantly 0 times; of these: 345384 (40.95%) aligned discordantly 1 time ---- 498003 pairs aligned 0 times concordantly or discordantly; of these: 996006 mates make up the pairs; of these: 773628 (77.67%) aligned 0 times 50173 (5.04%) aligned exactly 1 time 172205 (17.29%) aligned >1 times 88.76% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 123138 / 2917671 = 0.0422 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.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 @ Fri, 16 Oct 2020 08:10:19: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:10:19: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:10:26: 1000000 INFO @ Fri, 16 Oct 2020 08:10:33: 2000000 INFO @ Fri, 16 Oct 2020 08:10:41: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:10:48: 4000000 INFO @ Fri, 16 Oct 2020 08:10:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.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 @ Fri, 16 Oct 2020 08:10:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:10:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:10:56: 5000000 INFO @ Fri, 16 Oct 2020 08:10:57: 1000000 INFO @ Fri, 16 Oct 2020 08:11:04: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:11:04: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:11:04: #1 total tags in treatment: 2493392 INFO @ Fri, 16 Oct 2020 08:11:04: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:11:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:11:04: #1 tags after filtering in treatment: 1825912 INFO @ Fri, 16 Oct 2020 08:11:04: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 16 Oct 2020 08:11:04: #1 finished! INFO @ Fri, 16 Oct 2020 08:11:04: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:11:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:11:04: #2 number of paired peaks: 256 WARNING @ Fri, 16 Oct 2020 08:11:04: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 16 Oct 2020 08:11:04: start model_add_line... INFO @ Fri, 16 Oct 2020 08:11:04: start X-correlation... INFO @ Fri, 16 Oct 2020 08:11:04: end of X-cor INFO @ Fri, 16 Oct 2020 08:11:04: #2 finished! INFO @ Fri, 16 Oct 2020 08:11:04: #2 predicted fragment length is 172 bps INFO @ Fri, 16 Oct 2020 08:11:04: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 16 Oct 2020 08:11:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05_model.r WARNING @ Fri, 16 Oct 2020 08:11:04: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:11:04: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 16 Oct 2020 08:11:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:11:04: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:11:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:11:05: 2000000 INFO @ Fri, 16 Oct 2020 08:11:08: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:11:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:11:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:11:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05_summits.bed INFO @ Fri, 16 Oct 2020 08:11:10: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1445 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:11:13: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:11:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.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 @ Fri, 16 Oct 2020 08:11:19: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:11:19: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:11:21: 4000000 INFO @ Fri, 16 Oct 2020 08:11:27: 1000000 INFO @ Fri, 16 Oct 2020 08:11:29: 5000000 INFO @ Fri, 16 Oct 2020 08:11:35: 2000000 INFO @ Fri, 16 Oct 2020 08:11:36: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:11:36: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:11:36: #1 total tags in treatment: 2493392 INFO @ Fri, 16 Oct 2020 08:11:36: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:11:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:11:36: #1 tags after filtering in treatment: 1825912 INFO @ Fri, 16 Oct 2020 08:11:36: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 16 Oct 2020 08:11:36: #1 finished! INFO @ Fri, 16 Oct 2020 08:11:36: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:11:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:11:36: #2 number of paired peaks: 256 WARNING @ Fri, 16 Oct 2020 08:11:36: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 16 Oct 2020 08:11:36: start model_add_line... INFO @ Fri, 16 Oct 2020 08:11:36: start X-correlation... INFO @ Fri, 16 Oct 2020 08:11:36: end of X-cor INFO @ Fri, 16 Oct 2020 08:11:36: #2 finished! INFO @ Fri, 16 Oct 2020 08:11:36: #2 predicted fragment length is 172 bps INFO @ Fri, 16 Oct 2020 08:11:36: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 16 Oct 2020 08:11:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10_model.r WARNING @ Fri, 16 Oct 2020 08:11:36: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:11:36: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 16 Oct 2020 08:11:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:11:36: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:11:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:11:41: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:11:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10_summits.bed INFO @ Fri, 16 Oct 2020 08:11:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1047 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:11:43: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:11:51: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:11:59: 5000000 INFO @ Fri, 16 Oct 2020 08:12:05: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:12:05: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:12:05: #1 total tags in treatment: 2493392 INFO @ Fri, 16 Oct 2020 08:12:05: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:12:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:12:05: #1 tags after filtering in treatment: 1825912 INFO @ Fri, 16 Oct 2020 08:12:05: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 16 Oct 2020 08:12:05: #1 finished! INFO @ Fri, 16 Oct 2020 08:12:05: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:12:05: #2 number of paired peaks: 256 WARNING @ Fri, 16 Oct 2020 08:12:05: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 16 Oct 2020 08:12:05: start model_add_line... INFO @ Fri, 16 Oct 2020 08:12:05: start X-correlation... INFO @ Fri, 16 Oct 2020 08:12:05: end of X-cor INFO @ Fri, 16 Oct 2020 08:12:05: #2 finished! INFO @ Fri, 16 Oct 2020 08:12:05: #2 predicted fragment length is 172 bps INFO @ Fri, 16 Oct 2020 08:12:05: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 16 Oct 2020 08:12:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20_model.r WARNING @ Fri, 16 Oct 2020 08:12:05: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:12:05: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 16 Oct 2020 08:12:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:12:05: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:12:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:12:10: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:12:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:12:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:12:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20_summits.bed INFO @ Fri, 16 Oct 2020 08:12:12: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (698 records, 4 fields): 4 millis CompletedMACS2peakCalling