Job ID = 10223818 SRX = ERX4439578 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:14:02 prefetch.2.10.7: 1) Downloading 'ERR4501507'... 2020-10-15T23:14:02 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:14:39 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:14:39 prefetch.2.10.7: 'ERR4501507' is valid 2020-10-15T23:14:39 prefetch.2.10.7: 1) 'ERR4501507' was downloaded successfully 2020-10-15T23:15:07 prefetch.2.10.7: 'ERR4501507' has 5 unresolved dependencies 2020-10-15T23:15:07 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:15:07 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:15:19 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:15:19 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:15:19 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:15:19 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:15:30 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:15:30 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:15:30 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:15:30 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:15:42 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:15:42 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:15:42 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:15:42 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:15:51 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:15:51 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:15:51 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:15:51 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:16:00 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:16:00 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3823833 spots for ERR4501507/ERR4501507.sra Written 3823833 spots for ERR4501507/ERR4501507.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: 00:02:44 3823833 reads; of these: 3823833 (100.00%) were paired; of these: 955528 (24.99%) aligned concordantly 0 times 2526752 (66.08%) aligned concordantly exactly 1 time 341553 (8.93%) aligned concordantly >1 times ---- 955528 pairs aligned concordantly 0 times; of these: 420354 (43.99%) aligned discordantly 1 time ---- 535174 pairs aligned 0 times concordantly or discordantly; of these: 1070348 mates make up the pairs; of these: 891561 (83.30%) aligned 0 times 58884 (5.50%) aligned exactly 1 time 119903 (11.20%) aligned >1 times 88.34% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 93369 / 3259449 = 0.0286 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 08:22:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.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 08:22:41: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:22:41: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:22:48: 1000000 INFO @ Fri, 16 Oct 2020 08:22:55: 2000000 INFO @ Fri, 16 Oct 2020 08:23:01: 3000000 INFO @ Fri, 16 Oct 2020 08:23:08: 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 08:23:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.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 08:23:11: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:23:11: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:23:15: 5000000 INFO @ Fri, 16 Oct 2020 08:23:19: 1000000 INFO @ Fri, 16 Oct 2020 08:23:22: 6000000 INFO @ Fri, 16 Oct 2020 08:23:26: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:23:26: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:23:26: #1 total tags in treatment: 2795165 INFO @ Fri, 16 Oct 2020 08:23:26: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:23:26: #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 08:23:26: #1 tags after filtering in treatment: 2152459 INFO @ Fri, 16 Oct 2020 08:23:26: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 16 Oct 2020 08:23:26: #1 finished! INFO @ Fri, 16 Oct 2020 08:23:26: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:23:27: 2000000 INFO @ Fri, 16 Oct 2020 08:23:27: #2 number of paired peaks: 168 WARNING @ Fri, 16 Oct 2020 08:23:27: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 16 Oct 2020 08:23:27: start model_add_line... INFO @ Fri, 16 Oct 2020 08:23:27: start X-correlation... INFO @ Fri, 16 Oct 2020 08:23:27: end of X-cor INFO @ Fri, 16 Oct 2020 08:23:27: #2 finished! INFO @ Fri, 16 Oct 2020 08:23:27: #2 predicted fragment length is 179 bps INFO @ Fri, 16 Oct 2020 08:23:27: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 16 Oct 2020 08:23:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.05_model.r WARNING @ Fri, 16 Oct 2020 08:23:27: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:23:27: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Fri, 16 Oct 2020 08:23:27: #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 08:23:27: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:23:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:23:32: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:23:34: 3000000 INFO @ Fri, 16 Oct 2020 08:23:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:23:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:23:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.05_summits.bed INFO @ Fri, 16 Oct 2020 08:23:34: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1309 records, 4 fields): 4 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 08:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.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 08:23:41: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:23:41: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:23:41: 4000000 INFO @ Fri, 16 Oct 2020 08:23:49: 1000000 INFO @ Fri, 16 Oct 2020 08:23:49: 5000000 INFO @ Fri, 16 Oct 2020 08:23:56: 6000000 INFO @ Fri, 16 Oct 2020 08:23:57: 2000000 INFO @ Fri, 16 Oct 2020 08:24:00: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:24:00: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:24:00: #1 total tags in treatment: 2795165 INFO @ Fri, 16 Oct 2020 08:24:00: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:24:00: #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 08:24:00: #1 tags after filtering in treatment: 2152459 INFO @ Fri, 16 Oct 2020 08:24:00: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 16 Oct 2020 08:24:00: #1 finished! INFO @ Fri, 16 Oct 2020 08:24:00: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:24:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:24:00: #2 number of paired peaks: 168 WARNING @ Fri, 16 Oct 2020 08:24:00: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 16 Oct 2020 08:24:00: start model_add_line... INFO @ Fri, 16 Oct 2020 08:24:00: start X-correlation... INFO @ Fri, 16 Oct 2020 08:24:00: end of X-cor INFO @ Fri, 16 Oct 2020 08:24:00: #2 finished! INFO @ Fri, 16 Oct 2020 08:24:00: #2 predicted fragment length is 179 bps INFO @ Fri, 16 Oct 2020 08:24:00: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 16 Oct 2020 08:24:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.10_model.r WARNING @ Fri, 16 Oct 2020 08:24:00: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:24:00: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Fri, 16 Oct 2020 08:24:00: #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 08:24:00: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:24:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:24:04: 3000000 INFO @ Fri, 16 Oct 2020 08:24:06: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:24:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:24:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.10_summits.bed INFO @ Fri, 16 Oct 2020 08:24:08: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (963 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:24:11: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:24:19: 5000000 INFO @ Fri, 16 Oct 2020 08:24:25: 6000000 INFO @ Fri, 16 Oct 2020 08:24:29: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:24:29: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:24:29: #1 total tags in treatment: 2795165 INFO @ Fri, 16 Oct 2020 08:24:29: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:24:29: #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 08:24:29: #1 tags after filtering in treatment: 2152459 INFO @ Fri, 16 Oct 2020 08:24:29: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 16 Oct 2020 08:24:29: #1 finished! INFO @ Fri, 16 Oct 2020 08:24:29: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:24:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:24:29: #2 number of paired peaks: 168 WARNING @ Fri, 16 Oct 2020 08:24:29: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 16 Oct 2020 08:24:29: start model_add_line... INFO @ Fri, 16 Oct 2020 08:24:29: start X-correlation... INFO @ Fri, 16 Oct 2020 08:24:29: end of X-cor INFO @ Fri, 16 Oct 2020 08:24:29: #2 finished! INFO @ Fri, 16 Oct 2020 08:24:29: #2 predicted fragment length is 179 bps INFO @ Fri, 16 Oct 2020 08:24:29: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 16 Oct 2020 08:24:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.20_model.r WARNING @ Fri, 16 Oct 2020 08:24:29: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:24:29: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Fri, 16 Oct 2020 08:24:29: #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 08:24:29: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:24:35: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439578/ERX4439578.20_summits.bed INFO @ Fri, 16 Oct 2020 08:24:37: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (658 records, 4 fields): 3 millis CompletedMACS2peakCalling