Job ID = 10223899 SRX = ERX4439640 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:41:29 prefetch.2.10.7: 1) Downloading 'ERR4501569'... 2020-10-15T23:41:29 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:42:16 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:42:16 prefetch.2.10.7: 'ERR4501569' is valid 2020-10-15T23:42:16 prefetch.2.10.7: 1) 'ERR4501569' was downloaded successfully 2020-10-15T23:42:44 prefetch.2.10.7: 'ERR4501569' has 5 unresolved dependencies 2020-10-15T23:42:44 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:42:44 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:43:08 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:43:08 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:43:08 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:43:08 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:43:16 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:43:16 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:43:16 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:43:16 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:43:27 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:43:27 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:43:27 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:43:27 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:43:39 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:43:39 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:43:39 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:43:39 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:43:55 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:43:55 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3838079 spots for ERR4501569/ERR4501569.sra Written 3838079 spots for ERR4501569/ERR4501569.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: 00:02:59 3838079 reads; of these: 3838079 (100.00%) were paired; of these: 1031030 (26.86%) aligned concordantly 0 times 2402983 (62.61%) aligned concordantly exactly 1 time 404066 (10.53%) aligned concordantly >1 times ---- 1031030 pairs aligned concordantly 0 times; of these: 453695 (44.00%) aligned discordantly 1 time ---- 577335 pairs aligned 0 times concordantly or discordantly; of these: 1154670 mates make up the pairs; of these: 925747 (80.17%) aligned 0 times 64698 (5.60%) aligned exactly 1 time 164225 (14.22%) aligned >1 times 87.94% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 56052 / 3229515 = 0.0174 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 08:50:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.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 08:50:52: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:50:52: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:50:59: 1000000 INFO @ Fri, 16 Oct 2020 08:51:06: 2000000 INFO @ Fri, 16 Oct 2020 08:51:13: 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 08:51:21: 4000000 INFO @ Fri, 16 Oct 2020 08:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.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 08:51:21: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:51:21: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:51:28: 5000000 INFO @ Fri, 16 Oct 2020 08:51:29: 1000000 INFO @ Fri, 16 Oct 2020 08:51:35: 6000000 INFO @ Fri, 16 Oct 2020 08:51:36: 2000000 INFO @ Fri, 16 Oct 2020 08:51:40: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:51:40: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:51:40: #1 total tags in treatment: 2759090 INFO @ Fri, 16 Oct 2020 08:51:40: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:51:40: #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 08:51:40: #1 tags after filtering in treatment: 2389255 INFO @ Fri, 16 Oct 2020 08:51:40: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 08:51:40: #1 finished! INFO @ Fri, 16 Oct 2020 08:51:40: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:51:40: #2 number of paired peaks: 112 WARNING @ Fri, 16 Oct 2020 08:51:40: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Fri, 16 Oct 2020 08:51:40: start model_add_line... INFO @ Fri, 16 Oct 2020 08:51:40: start X-correlation... INFO @ Fri, 16 Oct 2020 08:51:40: end of X-cor INFO @ Fri, 16 Oct 2020 08:51:40: #2 finished! INFO @ Fri, 16 Oct 2020 08:51:40: #2 predicted fragment length is 158 bps INFO @ Fri, 16 Oct 2020 08:51:40: #2 alternative fragment length(s) may be 1,158,206,523,556,581 bps INFO @ Fri, 16 Oct 2020 08:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05_model.r WARNING @ Fri, 16 Oct 2020 08:51:40: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:51:40: #2 You may need to consider one of the other alternative d(s): 1,158,206,523,556,581 WARNING @ Fri, 16 Oct 2020 08:51:40: #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 08:51:40: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:51:43: 3000000 INFO @ Fri, 16 Oct 2020 08:51:45: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:51:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:51:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:51:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.05_summits.bed INFO @ Fri, 16 Oct 2020 08:51:47: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (39 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 08:51:50: 4000000 INFO @ Fri, 16 Oct 2020 08:51:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.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 08:51:52: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:51:52: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:51:57: 5000000 INFO @ Fri, 16 Oct 2020 08:51:59: 1000000 INFO @ Fri, 16 Oct 2020 08:52:04: 6000000 INFO @ Fri, 16 Oct 2020 08:52:06: 2000000 INFO @ Fri, 16 Oct 2020 08:52:09: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:52:09: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:52:09: #1 total tags in treatment: 2759090 INFO @ Fri, 16 Oct 2020 08:52:09: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:52:09: #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 08:52:09: #1 tags after filtering in treatment: 2389255 INFO @ Fri, 16 Oct 2020 08:52:09: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 08:52:09: #1 finished! INFO @ Fri, 16 Oct 2020 08:52:09: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:52:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:52:09: #2 number of paired peaks: 112 WARNING @ Fri, 16 Oct 2020 08:52:09: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Fri, 16 Oct 2020 08:52:09: start model_add_line... INFO @ Fri, 16 Oct 2020 08:52:09: start X-correlation... INFO @ Fri, 16 Oct 2020 08:52:09: end of X-cor INFO @ Fri, 16 Oct 2020 08:52:09: #2 finished! INFO @ Fri, 16 Oct 2020 08:52:09: #2 predicted fragment length is 158 bps INFO @ Fri, 16 Oct 2020 08:52:09: #2 alternative fragment length(s) may be 1,158,206,523,556,581 bps INFO @ Fri, 16 Oct 2020 08:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10_model.r WARNING @ Fri, 16 Oct 2020 08:52:09: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:52:09: #2 You may need to consider one of the other alternative d(s): 1,158,206,523,556,581 WARNING @ Fri, 16 Oct 2020 08:52:09: #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 08:52:09: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:52:13: 3000000 INFO @ Fri, 16 Oct 2020 08:52:14: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:52:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:52:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:52:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.10_summits.bed INFO @ Fri, 16 Oct 2020 08:52:16: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:52:20: 4000000 INFO @ Fri, 16 Oct 2020 08:52:27: 5000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:52:35: 6000000 INFO @ Fri, 16 Oct 2020 08:52:39: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:52:39: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:52:39: #1 total tags in treatment: 2759090 INFO @ Fri, 16 Oct 2020 08:52:39: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:52:39: #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 08:52:39: #1 tags after filtering in treatment: 2389255 INFO @ Fri, 16 Oct 2020 08:52:39: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 08:52:39: #1 finished! INFO @ Fri, 16 Oct 2020 08:52:39: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:52:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:52:39: #2 number of paired peaks: 112 WARNING @ Fri, 16 Oct 2020 08:52:39: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Fri, 16 Oct 2020 08:52:39: start model_add_line... INFO @ Fri, 16 Oct 2020 08:52:39: start X-correlation... INFO @ Fri, 16 Oct 2020 08:52:39: end of X-cor INFO @ Fri, 16 Oct 2020 08:52:39: #2 finished! INFO @ Fri, 16 Oct 2020 08:52:39: #2 predicted fragment length is 158 bps INFO @ Fri, 16 Oct 2020 08:52:39: #2 alternative fragment length(s) may be 1,158,206,523,556,581 bps INFO @ Fri, 16 Oct 2020 08:52:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20_model.r WARNING @ Fri, 16 Oct 2020 08:52:39: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:52:39: #2 You may need to consider one of the other alternative d(s): 1,158,206,523,556,581 WARNING @ Fri, 16 Oct 2020 08:52:39: #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 08:52:39: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:52:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:52:44: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:52:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:52:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:52:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439640/ERX4439640.20_summits.bed INFO @ Fri, 16 Oct 2020 08:52:46: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling