Job ID = 10223767 SRX = ERX4439549 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T22:52:08 prefetch.2.10.7: 1) Downloading 'ERR4501478'... 2020-10-15T22:52:08 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:52:42 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:52:42 prefetch.2.10.7: 'ERR4501478' is valid 2020-10-15T22:52:42 prefetch.2.10.7: 1) 'ERR4501478' was downloaded successfully 2020-10-15T22:53:10 prefetch.2.10.7: 'ERR4501478' has 5 unresolved dependencies 2020-10-15T22:53:10 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T22:53:10 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:53:18 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:53:18 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T22:53:18 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T22:53:18 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:53:26 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:53:26 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T22:53:26 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T22:53:26 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:53:35 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:53:35 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T22:53:35 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T22:53:35 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:53:42 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:53:42 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T22:53:42 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T22:53:42 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T22:53:49 prefetch.2.10.7: HTTPS download succeed 2020-10-15T22:53:49 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3169264 spots for ERR4501478/ERR4501478.sra Written 3169264 spots for ERR4501478/ERR4501478.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: 00:03:12 3169264 reads; of these: 3169264 (100.00%) were paired; of these: 1583154 (49.95%) aligned concordantly 0 times 1306139 (41.21%) aligned concordantly exactly 1 time 279971 (8.83%) aligned concordantly >1 times ---- 1583154 pairs aligned concordantly 0 times; of these: 295275 (18.65%) aligned discordantly 1 time ---- 1287879 pairs aligned 0 times concordantly or discordantly; of these: 2575758 mates make up the pairs; of these: 2018789 (78.38%) aligned 0 times 251629 (9.77%) aligned exactly 1 time 305340 (11.85%) aligned >1 times 68.15% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 112704 / 1847047 = 0.0610 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 07:59:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.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 07:59:56: #1 read tag files... INFO @ Fri, 16 Oct 2020 07:59:56: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:00:02: 1000000 INFO @ Fri, 16 Oct 2020 08:00:08: 2000000 INFO @ Fri, 16 Oct 2020 08:00:14: 3000000 INFO @ Fri, 16 Oct 2020 08:00:20: 4000000 INFO @ Fri, 16 Oct 2020 08:00:21: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:00:21: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:00:21: #1 total tags in treatment: 1493725 INFO @ Fri, 16 Oct 2020 08:00:21: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:00:21: #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 08:00:21: #1 tags after filtering in treatment: 1175951 INFO @ Fri, 16 Oct 2020 08:00:21: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 16 Oct 2020 08:00:21: #1 finished! INFO @ Fri, 16 Oct 2020 08:00:21: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:00:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:00:21: #2 number of paired peaks: 243 WARNING @ Fri, 16 Oct 2020 08:00:21: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Fri, 16 Oct 2020 08:00:21: start model_add_line... INFO @ Fri, 16 Oct 2020 08:00:21: start X-correlation... INFO @ Fri, 16 Oct 2020 08:00:21: end of X-cor INFO @ Fri, 16 Oct 2020 08:00:21: #2 finished! INFO @ Fri, 16 Oct 2020 08:00:21: #2 predicted fragment length is 160 bps INFO @ Fri, 16 Oct 2020 08:00:21: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 16 Oct 2020 08:00:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05_model.r WARNING @ Fri, 16 Oct 2020 08:00:21: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:00:21: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Fri, 16 Oct 2020 08:00:21: #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 08:00:21: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:00:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:00:24: #3 Call peaks for each chromosome... 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 08:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05_summits.bed INFO @ Fri, 16 Oct 2020 08:00:25: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (867 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.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 08:00:26: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:00:26: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:00:32: 1000000 INFO @ Fri, 16 Oct 2020 08:00:38: 2000000 INFO @ Fri, 16 Oct 2020 08:00:44: 3000000 INFO @ Fri, 16 Oct 2020 08:00:50: 4000000 INFO @ Fri, 16 Oct 2020 08:00:51: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:00:51: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:00:51: #1 total tags in treatment: 1493725 INFO @ Fri, 16 Oct 2020 08:00:51: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:00:51: #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 08:00:51: #1 tags after filtering in treatment: 1175951 INFO @ Fri, 16 Oct 2020 08:00:51: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 16 Oct 2020 08:00:51: #1 finished! INFO @ Fri, 16 Oct 2020 08:00:51: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:00:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:00:51: #2 number of paired peaks: 243 WARNING @ Fri, 16 Oct 2020 08:00:51: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Fri, 16 Oct 2020 08:00:51: start model_add_line... INFO @ Fri, 16 Oct 2020 08:00:51: start X-correlation... INFO @ Fri, 16 Oct 2020 08:00:51: end of X-cor INFO @ Fri, 16 Oct 2020 08:00:51: #2 finished! INFO @ Fri, 16 Oct 2020 08:00:51: #2 predicted fragment length is 160 bps INFO @ Fri, 16 Oct 2020 08:00:51: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 16 Oct 2020 08:00:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10_model.r WARNING @ Fri, 16 Oct 2020 08:00:51: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:00:51: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Fri, 16 Oct 2020 08:00:51: #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 08:00:51: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:00:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:00:54: #3 Call peaks for each chromosome... 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 08:00:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:00:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:00:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10_summits.bed INFO @ Fri, 16 Oct 2020 08:00:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (611 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.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 08:00:56: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:00:56: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:01:03: 1000000 INFO @ Fri, 16 Oct 2020 08:01:10: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:01:18: 3000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:01:25: 4000000 INFO @ Fri, 16 Oct 2020 08:01:26: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:01:26: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:01:26: #1 total tags in treatment: 1493725 INFO @ Fri, 16 Oct 2020 08:01:26: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:01:26: #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 08:01:26: #1 tags after filtering in treatment: 1175951 INFO @ Fri, 16 Oct 2020 08:01:26: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 16 Oct 2020 08:01:26: #1 finished! INFO @ Fri, 16 Oct 2020 08:01:26: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:01:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:01:26: #2 number of paired peaks: 243 WARNING @ Fri, 16 Oct 2020 08:01:26: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Fri, 16 Oct 2020 08:01:26: start model_add_line... INFO @ Fri, 16 Oct 2020 08:01:26: start X-correlation... INFO @ Fri, 16 Oct 2020 08:01:26: end of X-cor INFO @ Fri, 16 Oct 2020 08:01:26: #2 finished! INFO @ Fri, 16 Oct 2020 08:01:26: #2 predicted fragment length is 160 bps INFO @ Fri, 16 Oct 2020 08:01:26: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 16 Oct 2020 08:01:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20_model.r WARNING @ Fri, 16 Oct 2020 08:01:26: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:01:26: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Fri, 16 Oct 2020 08:01:26: #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 08:01:26: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:01:29: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:01:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:01:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20_summits.bed INFO @ Fri, 16 Oct 2020 08:01:30: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (433 records, 4 fields): 1 millis CompletedMACS2peakCalling