Job ID = 10223843 SRX = ERX4439596 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:22:05 prefetch.2.10.7: 1) Downloading 'ERR4501525'... 2020-10-15T23:22:05 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:22:54 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:22:55 prefetch.2.10.7: 'ERR4501525' is valid 2020-10-15T23:22:55 prefetch.2.10.7: 1) 'ERR4501525' was downloaded successfully 2020-10-15T23:23:23 prefetch.2.10.7: 'ERR4501525' has 5 unresolved dependencies 2020-10-15T23:23:23 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:23:23 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:23:33 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:23:33 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:23:33 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:23:33 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:23:45 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:23:45 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:23:45 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:23:45 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:23:57 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:23:57 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:23:57 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:23:57 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:24:09 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:24:09 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:24:09 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:24:09 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:24:19 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:24:19 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3435735 spots for ERR4501525/ERR4501525.sra Written 3435735 spots for ERR4501525/ERR4501525.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: 00:02:35 3435735 reads; of these: 3435735 (100.00%) were paired; of these: 1089802 (31.72%) aligned concordantly 0 times 2014509 (58.63%) aligned concordantly exactly 1 time 331424 (9.65%) aligned concordantly >1 times ---- 1089802 pairs aligned concordantly 0 times; of these: 464238 (42.60%) aligned discordantly 1 time ---- 625564 pairs aligned 0 times concordantly or discordantly; of these: 1251128 mates make up the pairs; of these: 1020911 (81.60%) aligned 0 times 67697 (5.41%) aligned exactly 1 time 162520 (12.99%) aligned >1 times 85.14% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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] 43700 / 2778990 = 0.0157 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 08:30:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.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 08:30:29: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:30:29: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:30:36: 1000000 INFO @ Fri, 16 Oct 2020 08:30:42: 2000000 INFO @ Fri, 16 Oct 2020 08:30:49: 3000000 INFO @ Fri, 16 Oct 2020 08:30:55: 4000000 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 08:30:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.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 08:30:59: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:30:59: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:31:02: 5000000 INFO @ Fri, 16 Oct 2020 08:31:08: 1000000 INFO @ Fri, 16 Oct 2020 08:31:08: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:31:08: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:31:08: #1 total tags in treatment: 2310708 INFO @ Fri, 16 Oct 2020 08:31:08: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:31:08: #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 08:31:08: #1 tags after filtering in treatment: 2018371 INFO @ Fri, 16 Oct 2020 08:31:08: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 08:31:08: #1 finished! INFO @ Fri, 16 Oct 2020 08:31:08: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:31:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:31:08: #2 number of paired peaks: 163 WARNING @ Fri, 16 Oct 2020 08:31:08: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 16 Oct 2020 08:31:08: start model_add_line... INFO @ Fri, 16 Oct 2020 08:31:08: start X-correlation... INFO @ Fri, 16 Oct 2020 08:31:08: end of X-cor INFO @ Fri, 16 Oct 2020 08:31:08: #2 finished! INFO @ Fri, 16 Oct 2020 08:31:08: #2 predicted fragment length is 161 bps INFO @ Fri, 16 Oct 2020 08:31:08: #2 alternative fragment length(s) may be 3,161,531,584 bps INFO @ Fri, 16 Oct 2020 08:31:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.05_model.r WARNING @ Fri, 16 Oct 2020 08:31:08: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:31:08: #2 You may need to consider one of the other alternative d(s): 3,161,531,584 WARNING @ Fri, 16 Oct 2020 08:31:08: #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 08:31:08: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:31:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:31:12: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.05_summits.bed INFO @ Fri, 16 Oct 2020 08:31:14: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (53 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:31:15: 2000000 INFO @ Fri, 16 Oct 2020 08:31:23: 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 08:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.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 08:31:29: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:31:29: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:31:30: 4000000 INFO @ Fri, 16 Oct 2020 08:31:37: 1000000 INFO @ Fri, 16 Oct 2020 08:31:38: 5000000 INFO @ Fri, 16 Oct 2020 08:31:44: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:31:44: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:31:44: #1 total tags in treatment: 2310708 INFO @ Fri, 16 Oct 2020 08:31:44: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:31:44: #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 08:31:44: #1 tags after filtering in treatment: 2018371 INFO @ Fri, 16 Oct 2020 08:31:44: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 08:31:44: #1 finished! INFO @ Fri, 16 Oct 2020 08:31:44: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:31:44: #2 number of paired peaks: 163 WARNING @ Fri, 16 Oct 2020 08:31:44: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 16 Oct 2020 08:31:44: start model_add_line... INFO @ Fri, 16 Oct 2020 08:31:44: start X-correlation... INFO @ Fri, 16 Oct 2020 08:31:44: end of X-cor INFO @ Fri, 16 Oct 2020 08:31:44: #2 finished! INFO @ Fri, 16 Oct 2020 08:31:44: #2 predicted fragment length is 161 bps INFO @ Fri, 16 Oct 2020 08:31:44: #2 alternative fragment length(s) may be 3,161,531,584 bps INFO @ Fri, 16 Oct 2020 08:31:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.10_model.r WARNING @ Fri, 16 Oct 2020 08:31:44: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:31:44: #2 You may need to consider one of the other alternative d(s): 3,161,531,584 WARNING @ Fri, 16 Oct 2020 08:31:44: #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 08:31:44: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:31:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:31:45: 2000000 INFO @ Fri, 16 Oct 2020 08:31:48: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.10_summits.bed INFO @ Fri, 16 Oct 2020 08:31:50: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (27 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:31:52: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:31:59: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:32:06: 5000000 INFO @ Fri, 16 Oct 2020 08:32:12: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:32:12: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:32:12: #1 total tags in treatment: 2310708 INFO @ Fri, 16 Oct 2020 08:32:12: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:32:12: #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 08:32:12: #1 tags after filtering in treatment: 2018371 INFO @ Fri, 16 Oct 2020 08:32:12: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 08:32:12: #1 finished! INFO @ Fri, 16 Oct 2020 08:32:12: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:32:12: #2 number of paired peaks: 163 WARNING @ Fri, 16 Oct 2020 08:32:12: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 16 Oct 2020 08:32:12: start model_add_line... INFO @ Fri, 16 Oct 2020 08:32:12: start X-correlation... INFO @ Fri, 16 Oct 2020 08:32:12: end of X-cor INFO @ Fri, 16 Oct 2020 08:32:12: #2 finished! INFO @ Fri, 16 Oct 2020 08:32:12: #2 predicted fragment length is 161 bps INFO @ Fri, 16 Oct 2020 08:32:12: #2 alternative fragment length(s) may be 3,161,531,584 bps INFO @ Fri, 16 Oct 2020 08:32:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.20_model.r WARNING @ Fri, 16 Oct 2020 08:32:12: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:32:12: #2 You may need to consider one of the other alternative d(s): 3,161,531,584 WARNING @ Fri, 16 Oct 2020 08:32:12: #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 08:32:12: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:32:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:32:16: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:32:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:32:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:32:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439596/ERX4439596.20_summits.bed INFO @ Fri, 16 Oct 2020 08:32:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling