Job ID = 10223769 SRX = ERX4439550 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T22:54:01 prefetch.2.10.7: 1) Downloading 'ERR4501479'... 2020-10-15T22:54:01 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:54:32 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:54:33 prefetch.2.10.7: 'ERR4501479' is valid 2020-10-15T22:54:33 prefetch.2.10.7: 1) 'ERR4501479' was downloaded successfully 2020-10-15T22:55:01 prefetch.2.10.7: 'ERR4501479' has 5 unresolved dependencies 2020-10-15T22:55:01 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T22:55:01 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:55:13 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:55:13 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T22:55:13 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T22:55:13 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:55:25 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:55:25 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T22:55:25 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T22:55:25 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:55:38 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:55:38 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T22:55:38 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T22:55:38 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:55:45 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:55:45 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T22:55:45 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T22:55:45 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:55:52 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:55:52 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 2847796 spots for ERR4501479/ERR4501479.sra Written 2847796 spots for ERR4501479/ERR4501479.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: 00:02:55 2847796 reads; of these: 2847796 (100.00%) were paired; of these: 1552262 (54.51%) aligned concordantly 0 times 1015572 (35.66%) aligned concordantly exactly 1 time 279962 (9.83%) aligned concordantly >1 times ---- 1552262 pairs aligned concordantly 0 times; of these: 278838 (17.96%) aligned discordantly 1 time ---- 1273424 pairs aligned 0 times concordantly or discordantly; of these: 2546848 mates make up the pairs; of these: 2025176 (79.52%) aligned 0 times 230275 (9.04%) aligned exactly 1 time 291397 (11.44%) aligned >1 times 64.44% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 175161 / 1539151 = 0.1138 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 08:01:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.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 08:01:18: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:01:18: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:01:25: 1000000 INFO @ Fri, 16 Oct 2020 08:01:32: 2000000 INFO @ Fri, 16 Oct 2020 08:01:38: 3000000 INFO @ Fri, 16 Oct 2020 08:01:40: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:01:40: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:01:40: #1 total tags in treatment: 1157399 INFO @ Fri, 16 Oct 2020 08:01:40: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:01:40: #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 08:01:40: #1 tags after filtering in treatment: 822658 INFO @ Fri, 16 Oct 2020 08:01:40: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 16 Oct 2020 08:01:40: #1 finished! INFO @ Fri, 16 Oct 2020 08:01:40: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:01:40: #2 number of paired peaks: 345 WARNING @ Fri, 16 Oct 2020 08:01:40: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Fri, 16 Oct 2020 08:01:40: start model_add_line... INFO @ Fri, 16 Oct 2020 08:01:40: start X-correlation... INFO @ Fri, 16 Oct 2020 08:01:40: end of X-cor INFO @ Fri, 16 Oct 2020 08:01:40: #2 finished! INFO @ Fri, 16 Oct 2020 08:01:40: #2 predicted fragment length is 150 bps INFO @ Fri, 16 Oct 2020 08:01:40: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 16 Oct 2020 08:01:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.05_model.r WARNING @ Fri, 16 Oct 2020 08:01:40: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:01:40: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 16 Oct 2020 08:01:40: #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 08:01:40: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:01:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:01:42: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:01:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:01:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:01:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.05_summits.bed INFO @ Fri, 16 Oct 2020 08:01:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (626 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 08:01:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.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 08:01:48: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:01:48: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:01:55: 1000000 INFO @ Fri, 16 Oct 2020 08:02:02: 2000000 INFO @ Fri, 16 Oct 2020 08:02:08: 3000000 INFO @ Fri, 16 Oct 2020 08:02:10: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:02:10: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:02:10: #1 total tags in treatment: 1157399 INFO @ Fri, 16 Oct 2020 08:02:10: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:02:10: #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 08:02:10: #1 tags after filtering in treatment: 822658 INFO @ Fri, 16 Oct 2020 08:02:10: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 16 Oct 2020 08:02:10: #1 finished! INFO @ Fri, 16 Oct 2020 08:02:10: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:02:11: #2 number of paired peaks: 345 WARNING @ Fri, 16 Oct 2020 08:02:11: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Fri, 16 Oct 2020 08:02:11: start model_add_line... INFO @ Fri, 16 Oct 2020 08:02:11: start X-correlation... INFO @ Fri, 16 Oct 2020 08:02:11: end of X-cor INFO @ Fri, 16 Oct 2020 08:02:11: #2 finished! INFO @ Fri, 16 Oct 2020 08:02:11: #2 predicted fragment length is 150 bps INFO @ Fri, 16 Oct 2020 08:02:11: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 16 Oct 2020 08:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.10_model.r WARNING @ Fri, 16 Oct 2020 08:02:11: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:02:11: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 16 Oct 2020 08:02:11: #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 08:02:11: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:02:13: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:02:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:02:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:02:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.10_summits.bed INFO @ Fri, 16 Oct 2020 08:02:14: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (507 records, 4 fields): 3 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 08:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.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 08:02:18: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:02:18: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:02:25: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:02:32: 2000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:02:39: 3000000 INFO @ Fri, 16 Oct 2020 08:02:41: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:02:41: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:02:41: #1 total tags in treatment: 1157399 INFO @ Fri, 16 Oct 2020 08:02:41: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:02:41: #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 08:02:41: #1 tags after filtering in treatment: 822658 INFO @ Fri, 16 Oct 2020 08:02:41: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 16 Oct 2020 08:02:41: #1 finished! INFO @ Fri, 16 Oct 2020 08:02:41: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:02:41: #2 number of paired peaks: 345 WARNING @ Fri, 16 Oct 2020 08:02:41: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Fri, 16 Oct 2020 08:02:41: start model_add_line... INFO @ Fri, 16 Oct 2020 08:02:41: start X-correlation... INFO @ Fri, 16 Oct 2020 08:02:41: end of X-cor INFO @ Fri, 16 Oct 2020 08:02:41: #2 finished! INFO @ Fri, 16 Oct 2020 08:02:41: #2 predicted fragment length is 150 bps INFO @ Fri, 16 Oct 2020 08:02:41: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 16 Oct 2020 08:02:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.20_model.r WARNING @ Fri, 16 Oct 2020 08:02:41: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:02:41: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 16 Oct 2020 08:02:41: #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 08:02:41: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:02:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:02:43: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:02:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:02:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:02:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439550/ERX4439550.20_summits.bed INFO @ Fri, 16 Oct 2020 08:02:44: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (416 records, 4 fields): 3 millis CompletedMACS2peakCalling