Job ID = 10223856 SRX = ERX4439606 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:28:14 prefetch.2.10.7: 1) Downloading 'ERR4501535'... 2020-10-15T23:28:14 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:28:48 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:28:49 prefetch.2.10.7: 'ERR4501535' is valid 2020-10-15T23:28:49 prefetch.2.10.7: 1) 'ERR4501535' was downloaded successfully 2020-10-15T23:29:16 prefetch.2.10.7: 'ERR4501535' has 5 unresolved dependencies 2020-10-15T23:29:16 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:29:16 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:29:25 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:29:25 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:29:25 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:29:25 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:29:36 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:29:36 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:29:36 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:29:36 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:29:48 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:29:48 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:29:48 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:29:48 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:29:56 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:29:56 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:29:56 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:29:56 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:30:03 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:30:03 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3748791 spots for ERR4501535/ERR4501535.sra Written 3748791 spots for ERR4501535/ERR4501535.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: 00:02:51 3748791 reads; of these: 3748791 (100.00%) were paired; of these: 1038457 (27.70%) aligned concordantly 0 times 2349182 (62.67%) aligned concordantly exactly 1 time 361152 (9.63%) aligned concordantly >1 times ---- 1038457 pairs aligned concordantly 0 times; of these: 484868 (46.69%) aligned discordantly 1 time ---- 553589 pairs aligned 0 times concordantly or discordantly; of these: 1107178 mates make up the pairs; of these: 883905 (79.83%) aligned 0 times 67282 (6.08%) aligned exactly 1 time 155991 (14.09%) aligned >1 times 88.21% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 48403 / 3162092 = 0.0153 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 08:36:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.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 08:36:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:36:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:36:54: 1000000 INFO @ Fri, 16 Oct 2020 08:36:59: 2000000 INFO @ Fri, 16 Oct 2020 08:37:04: 3000000 INFO @ Fri, 16 Oct 2020 08:37:10: 4000000 INFO @ Fri, 16 Oct 2020 08:37:15: 5000000 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 08:37:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.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 08:37:19: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:37:19: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:37:20: 6000000 INFO @ Fri, 16 Oct 2020 08:37:23: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:37:23: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:37:23: #1 total tags in treatment: 2670006 INFO @ Fri, 16 Oct 2020 08:37:23: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:37:23: #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 08:37:23: #1 tags after filtering in treatment: 2344337 INFO @ Fri, 16 Oct 2020 08:37:23: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 16 Oct 2020 08:37:23: #1 finished! INFO @ Fri, 16 Oct 2020 08:37:23: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:37:23: #2 number of paired peaks: 132 WARNING @ Fri, 16 Oct 2020 08:37:23: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 16 Oct 2020 08:37:23: start model_add_line... INFO @ Fri, 16 Oct 2020 08:37:23: start X-correlation... INFO @ Fri, 16 Oct 2020 08:37:23: end of X-cor INFO @ Fri, 16 Oct 2020 08:37:23: #2 finished! INFO @ Fri, 16 Oct 2020 08:37:23: #2 predicted fragment length is 154 bps INFO @ Fri, 16 Oct 2020 08:37:23: #2 alternative fragment length(s) may be 0,154,172,174,203,278,575,591 bps INFO @ Fri, 16 Oct 2020 08:37:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.05_model.r WARNING @ Fri, 16 Oct 2020 08:37:23: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:37:23: #2 You may need to consider one of the other alternative d(s): 0,154,172,174,203,278,575,591 WARNING @ Fri, 16 Oct 2020 08:37:23: #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 08:37:23: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:37:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:37:24: 1000000 INFO @ Fri, 16 Oct 2020 08:37:28: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:37:29: 2000000 INFO @ Fri, 16 Oct 2020 08:37:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:37:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:37:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.05_summits.bed INFO @ Fri, 16 Oct 2020 08:37:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:37:35: 3000000 INFO @ Fri, 16 Oct 2020 08:37:40: 4000000 INFO @ Fri, 16 Oct 2020 08:37:45: 5000000 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 08:37:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.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 08:37:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:37:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:37:50: 6000000 INFO @ Fri, 16 Oct 2020 08:37:53: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:37:53: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:37:53: #1 total tags in treatment: 2670006 INFO @ Fri, 16 Oct 2020 08:37:53: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:37:53: #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 08:37:53: #1 tags after filtering in treatment: 2344337 INFO @ Fri, 16 Oct 2020 08:37:53: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 16 Oct 2020 08:37:53: #1 finished! INFO @ Fri, 16 Oct 2020 08:37:53: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:37:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:37:53: #2 number of paired peaks: 132 WARNING @ Fri, 16 Oct 2020 08:37:53: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 16 Oct 2020 08:37:53: start model_add_line... INFO @ Fri, 16 Oct 2020 08:37:53: start X-correlation... INFO @ Fri, 16 Oct 2020 08:37:53: end of X-cor INFO @ Fri, 16 Oct 2020 08:37:53: #2 finished! INFO @ Fri, 16 Oct 2020 08:37:53: #2 predicted fragment length is 154 bps INFO @ Fri, 16 Oct 2020 08:37:53: #2 alternative fragment length(s) may be 0,154,172,174,203,278,575,591 bps INFO @ Fri, 16 Oct 2020 08:37:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.10_model.r WARNING @ Fri, 16 Oct 2020 08:37:53: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:37:53: #2 You may need to consider one of the other alternative d(s): 0,154,172,174,203,278,575,591 WARNING @ Fri, 16 Oct 2020 08:37:53: #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 08:37:53: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:37:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:37:54: 1000000 INFO @ Fri, 16 Oct 2020 08:37:58: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:37:59: 2000000 INFO @ Fri, 16 Oct 2020 08:38:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:38:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:38:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.10_summits.bed INFO @ Fri, 16 Oct 2020 08:38:00: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (21 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:38:05: 3000000 INFO @ Fri, 16 Oct 2020 08:38:10: 4000000 INFO @ Fri, 16 Oct 2020 08:38:15: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:38:20: 6000000 INFO @ Fri, 16 Oct 2020 08:38:23: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:38:23: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:38:23: #1 total tags in treatment: 2670006 INFO @ Fri, 16 Oct 2020 08:38:23: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:38:23: #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 08:38:23: #1 tags after filtering in treatment: 2344337 INFO @ Fri, 16 Oct 2020 08:38:23: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 16 Oct 2020 08:38:23: #1 finished! INFO @ Fri, 16 Oct 2020 08:38:23: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:38:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:38:23: #2 number of paired peaks: 132 WARNING @ Fri, 16 Oct 2020 08:38:23: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 16 Oct 2020 08:38:23: start model_add_line... INFO @ Fri, 16 Oct 2020 08:38:23: start X-correlation... INFO @ Fri, 16 Oct 2020 08:38:23: end of X-cor INFO @ Fri, 16 Oct 2020 08:38:23: #2 finished! INFO @ Fri, 16 Oct 2020 08:38:23: #2 predicted fragment length is 154 bps INFO @ Fri, 16 Oct 2020 08:38:23: #2 alternative fragment length(s) may be 0,154,172,174,203,278,575,591 bps INFO @ Fri, 16 Oct 2020 08:38:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.20_model.r WARNING @ Fri, 16 Oct 2020 08:38:23: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:38:23: #2 You may need to consider one of the other alternative d(s): 0,154,172,174,203,278,575,591 WARNING @ Fri, 16 Oct 2020 08:38:23: #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 08:38:23: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:38:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:38:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:38:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:38:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:38:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439606/ERX4439606.20_summits.bed INFO @ Fri, 16 Oct 2020 08:38:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling