Job ID = 10223853 SRX = ERX4439604 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:28:02 prefetch.2.10.7: 1) Downloading 'ERR4501533'... 2020-10-15T23:28:02 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:28:39 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:28:39 prefetch.2.10.7: 'ERR4501533' is valid 2020-10-15T23:28:39 prefetch.2.10.7: 1) 'ERR4501533' was downloaded successfully 2020-10-15T23:29:07 prefetch.2.10.7: 'ERR4501533' has 5 unresolved dependencies 2020-10-15T23:29:07 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:29:07 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:29:20 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:29:20 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:29:20 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:29:20 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:29:27 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:29:27 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:29:27 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:29:27 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:29:39 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:29:39 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:29:39 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:29:39 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:29:50 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:29:50 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:29:50 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:29:50 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:29:57 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:29:57 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 2532401 spots for ERR4501533/ERR4501533.sra Written 2532401 spots for ERR4501533/ERR4501533.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: 00:02:37 2532401 reads; of these: 2532401 (100.00%) were paired; of these: 1377192 (54.38%) aligned concordantly 0 times 879346 (34.72%) aligned concordantly exactly 1 time 275863 (10.89%) aligned concordantly >1 times ---- 1377192 pairs aligned concordantly 0 times; of these: 242287 (17.59%) aligned discordantly 1 time ---- 1134905 pairs aligned 0 times concordantly or discordantly; of these: 2269810 mates make up the pairs; of these: 1808417 (79.67%) aligned 0 times 189806 (8.36%) aligned exactly 1 time 271587 (11.97%) aligned >1 times 64.29% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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] 127939 / 1369311 = 0.0934 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 08:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.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 08:34:53: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:34:53: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:35:00: 1000000 INFO @ Fri, 16 Oct 2020 08:35:06: 2000000 INFO @ Fri, 16 Oct 2020 08:35:12: 3000000 INFO @ Fri, 16 Oct 2020 08:35:12: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:35:12: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:35:12: #1 total tags in treatment: 1056061 INFO @ Fri, 16 Oct 2020 08:35:12: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:35:12: #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 08:35:12: #1 tags after filtering in treatment: 696618 INFO @ Fri, 16 Oct 2020 08:35:12: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 16 Oct 2020 08:35:12: #1 finished! INFO @ Fri, 16 Oct 2020 08:35:12: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:35:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:35:12: #2 number of paired peaks: 525 WARNING @ Fri, 16 Oct 2020 08:35:12: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Fri, 16 Oct 2020 08:35:12: start model_add_line... INFO @ Fri, 16 Oct 2020 08:35:12: start X-correlation... INFO @ Fri, 16 Oct 2020 08:35:12: end of X-cor INFO @ Fri, 16 Oct 2020 08:35:12: #2 finished! INFO @ Fri, 16 Oct 2020 08:35:12: #2 predicted fragment length is 150 bps INFO @ Fri, 16 Oct 2020 08:35:12: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 16 Oct 2020 08:35:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.05_model.r WARNING @ Fri, 16 Oct 2020 08:35:12: #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 08:35:12: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 16 Oct 2020 08:35:12: #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 08:35:12: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:35:15: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:35:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:35:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:35:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.05_summits.bed INFO @ Fri, 16 Oct 2020 08:35:15: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (847 records, 4 fields): 2 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 08:35:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.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 08:35:23: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:35:23: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:35:29: 1000000 INFO @ Fri, 16 Oct 2020 08:35:34: 2000000 INFO @ Fri, 16 Oct 2020 08:35:40: 3000000 INFO @ Fri, 16 Oct 2020 08:35:40: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:35:40: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:35:40: #1 total tags in treatment: 1056061 INFO @ Fri, 16 Oct 2020 08:35:40: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:35:40: #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 08:35:40: #1 tags after filtering in treatment: 696618 INFO @ Fri, 16 Oct 2020 08:35:40: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 16 Oct 2020 08:35:40: #1 finished! INFO @ Fri, 16 Oct 2020 08:35:40: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:35:40: #2 number of paired peaks: 525 WARNING @ Fri, 16 Oct 2020 08:35:40: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Fri, 16 Oct 2020 08:35:40: start model_add_line... INFO @ Fri, 16 Oct 2020 08:35:40: start X-correlation... INFO @ Fri, 16 Oct 2020 08:35:40: end of X-cor INFO @ Fri, 16 Oct 2020 08:35:40: #2 finished! INFO @ Fri, 16 Oct 2020 08:35:40: #2 predicted fragment length is 150 bps INFO @ Fri, 16 Oct 2020 08:35:40: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 16 Oct 2020 08:35:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.10_model.r WARNING @ Fri, 16 Oct 2020 08:35:40: #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 08:35:40: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 16 Oct 2020 08:35:40: #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 08:35:40: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:35:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:35:42: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:35:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:35:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:35:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.10_summits.bed INFO @ Fri, 16 Oct 2020 08:35:43: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (722 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 08:35:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.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 08:35:53: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:35:53: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:35:59: 1000000 INFO @ Fri, 16 Oct 2020 08:36:04: 2000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:36:09: 3000000 INFO @ Fri, 16 Oct 2020 08:36:09: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:36:09: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:36:09: #1 total tags in treatment: 1056061 INFO @ Fri, 16 Oct 2020 08:36:09: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:36:09: #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 08:36:09: #1 tags after filtering in treatment: 696618 INFO @ Fri, 16 Oct 2020 08:36:09: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 16 Oct 2020 08:36:09: #1 finished! INFO @ Fri, 16 Oct 2020 08:36:09: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:36:10: #2 number of paired peaks: 525 WARNING @ Fri, 16 Oct 2020 08:36:10: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Fri, 16 Oct 2020 08:36:10: start model_add_line... INFO @ Fri, 16 Oct 2020 08:36:10: start X-correlation... INFO @ Fri, 16 Oct 2020 08:36:10: end of X-cor INFO @ Fri, 16 Oct 2020 08:36:10: #2 finished! INFO @ Fri, 16 Oct 2020 08:36:10: #2 predicted fragment length is 150 bps INFO @ Fri, 16 Oct 2020 08:36:10: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 16 Oct 2020 08:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.20_model.r WARNING @ Fri, 16 Oct 2020 08:36:10: #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 08:36:10: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 16 Oct 2020 08:36:10: #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 08:36:10: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:36:12: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:36:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:36:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:36:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439604/ERX4439604.20_summits.bed INFO @ Fri, 16 Oct 2020 08:36:12: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (564 records, 4 fields): 2 millis CompletedMACS2peakCalling