Job ID = 10223803 SRX = ERX4439567 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:08:12 prefetch.2.10.7: 1) Downloading 'ERR4501496'... 2020-10-15T23:08:12 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:08:47 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:08:48 prefetch.2.10.7: 'ERR4501496' is valid 2020-10-15T23:08:48 prefetch.2.10.7: 1) 'ERR4501496' was downloaded successfully 2020-10-15T23:09:15 prefetch.2.10.7: 'ERR4501496' has 5 unresolved dependencies 2020-10-15T23:09:15 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:09:15 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:09:28 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:09:28 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:09:28 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:09:28 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:09:35 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:09:35 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:09:35 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:09:35 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:09:48 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:09:48 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:09:48 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:09:48 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:09:59 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:09:59 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:09:59 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:09:59 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:10:09 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:10:09 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3437056 spots for ERR4501496/ERR4501496.sra Written 3437056 spots for ERR4501496/ERR4501496.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 3437056 reads; of these: 3437056 (100.00%) were paired; of these: 970507 (28.24%) aligned concordantly 0 times 2135833 (62.14%) aligned concordantly exactly 1 time 330716 (9.62%) aligned concordantly >1 times ---- 970507 pairs aligned concordantly 0 times; of these: 457977 (47.19%) aligned discordantly 1 time ---- 512530 pairs aligned 0 times concordantly or discordantly; of these: 1025060 mates make up the pairs; of these: 808159 (78.84%) aligned 0 times 60486 (5.90%) aligned exactly 1 time 156415 (15.26%) aligned >1 times 88.24% 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] 43071 / 2892633 = 0.0149 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 08:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.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 08:16:23: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:16:23: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:16:30: 1000000 INFO @ Fri, 16 Oct 2020 08:16:38: 2000000 INFO @ Fri, 16 Oct 2020 08:16:46: 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 08:16:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.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 08:16:53: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:16:53: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:16:54: 4000000 INFO @ Fri, 16 Oct 2020 08:17:02: 1000000 INFO @ Fri, 16 Oct 2020 08:17:02: 5000000 INFO @ Fri, 16 Oct 2020 08:17:09: 2000000 INFO @ Fri, 16 Oct 2020 08:17:10: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:17:10: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:17:10: #1 total tags in treatment: 2430779 INFO @ Fri, 16 Oct 2020 08:17:10: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:17:10: #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 08:17:10: #1 tags after filtering in treatment: 2159377 INFO @ Fri, 16 Oct 2020 08:17:10: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 08:17:10: #1 finished! INFO @ Fri, 16 Oct 2020 08:17:10: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:17:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:17:10: #2 number of paired peaks: 115 WARNING @ Fri, 16 Oct 2020 08:17:10: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 16 Oct 2020 08:17:10: start model_add_line... INFO @ Fri, 16 Oct 2020 08:17:10: start X-correlation... INFO @ Fri, 16 Oct 2020 08:17:10: end of X-cor INFO @ Fri, 16 Oct 2020 08:17:10: #2 finished! INFO @ Fri, 16 Oct 2020 08:17:10: #2 predicted fragment length is 140 bps INFO @ Fri, 16 Oct 2020 08:17:10: #2 alternative fragment length(s) may be 1,121,140,157,183,580 bps INFO @ Fri, 16 Oct 2020 08:17:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.05_model.r WARNING @ Fri, 16 Oct 2020 08:17:10: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:17:10: #2 You may need to consider one of the other alternative d(s): 1,121,140,157,183,580 WARNING @ Fri, 16 Oct 2020 08:17:10: #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 08:17:10: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:17:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:17:14: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:17:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:17:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:17:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.05_summits.bed INFO @ Fri, 16 Oct 2020 08:17:16: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:17:17: 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 08:17:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.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 08:17:23: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:17:23: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:17:25: 4000000 INFO @ Fri, 16 Oct 2020 08:17:30: 1000000 INFO @ Fri, 16 Oct 2020 08:17:33: 5000000 INFO @ Fri, 16 Oct 2020 08:17:38: 2000000 INFO @ Fri, 16 Oct 2020 08:17:41: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:17:41: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:17:41: #1 total tags in treatment: 2430779 INFO @ Fri, 16 Oct 2020 08:17:41: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:17:41: #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 08:17:41: #1 tags after filtering in treatment: 2159377 INFO @ Fri, 16 Oct 2020 08:17:41: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 08:17:41: #1 finished! INFO @ Fri, 16 Oct 2020 08:17:41: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:17:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:17:41: #2 number of paired peaks: 115 WARNING @ Fri, 16 Oct 2020 08:17:41: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 16 Oct 2020 08:17:41: start model_add_line... INFO @ Fri, 16 Oct 2020 08:17:41: start X-correlation... INFO @ Fri, 16 Oct 2020 08:17:41: end of X-cor INFO @ Fri, 16 Oct 2020 08:17:41: #2 finished! INFO @ Fri, 16 Oct 2020 08:17:41: #2 predicted fragment length is 140 bps INFO @ Fri, 16 Oct 2020 08:17:41: #2 alternative fragment length(s) may be 1,121,140,157,183,580 bps INFO @ Fri, 16 Oct 2020 08:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.10_model.r WARNING @ Fri, 16 Oct 2020 08:17:41: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:17:41: #2 You may need to consider one of the other alternative d(s): 1,121,140,157,183,580 WARNING @ Fri, 16 Oct 2020 08:17:41: #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 08:17:41: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:17:45: 3000000 INFO @ Fri, 16 Oct 2020 08:17:46: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:17:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:17:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:17:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.10_summits.bed INFO @ Fri, 16 Oct 2020 08:17:47: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:17:51: 4000000 INFO @ Fri, 16 Oct 2020 08:17:57: 5000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:18:04: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:18:04: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:18:04: #1 total tags in treatment: 2430779 INFO @ Fri, 16 Oct 2020 08:18:04: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:18:04: #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 08:18:04: #1 tags after filtering in treatment: 2159377 INFO @ Fri, 16 Oct 2020 08:18:04: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 08:18:04: #1 finished! INFO @ Fri, 16 Oct 2020 08:18:04: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:18:04: #2 number of paired peaks: 115 WARNING @ Fri, 16 Oct 2020 08:18:04: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 16 Oct 2020 08:18:04: start model_add_line... INFO @ Fri, 16 Oct 2020 08:18:04: start X-correlation... INFO @ Fri, 16 Oct 2020 08:18:04: end of X-cor INFO @ Fri, 16 Oct 2020 08:18:04: #2 finished! INFO @ Fri, 16 Oct 2020 08:18:04: #2 predicted fragment length is 140 bps INFO @ Fri, 16 Oct 2020 08:18:04: #2 alternative fragment length(s) may be 1,121,140,157,183,580 bps INFO @ Fri, 16 Oct 2020 08:18:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.20_model.r WARNING @ Fri, 16 Oct 2020 08:18:04: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:18:04: #2 You may need to consider one of the other alternative d(s): 1,121,140,157,183,580 WARNING @ Fri, 16 Oct 2020 08:18:04: #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 08:18:04: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:18:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:18:08: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:18:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:18:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:18:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439567/ERX4439567.20_summits.bed INFO @ Fri, 16 Oct 2020 08:18:10: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling