Job ID = 10223865 SRX = ERX4439612 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:31:44 prefetch.2.10.7: 1) Downloading 'ERR4501541'... 2020-10-15T23:31:44 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:32:15 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:32:16 prefetch.2.10.7: 'ERR4501541' is valid 2020-10-15T23:32:16 prefetch.2.10.7: 1) 'ERR4501541' was downloaded successfully 2020-10-15T23:32:44 prefetch.2.10.7: 'ERR4501541' has 5 unresolved dependencies 2020-10-15T23:32:44 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:32:44 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:32:56 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:32:56 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:32:56 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:32:56 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:33:04 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:33:04 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:33:04 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:33:04 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:33:16 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:33:16 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:33:16 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:33:16 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:33:28 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:33:28 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:33:28 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:33:28 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:33:38 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:33:38 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3442037 spots for ERR4501541/ERR4501541.sra Written 3442037 spots for ERR4501541/ERR4501541.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: 00:02:34 3442037 reads; of these: 3442037 (100.00%) were paired; of these: 845277 (24.56%) aligned concordantly 0 times 2095384 (60.88%) aligned concordantly exactly 1 time 501376 (14.57%) aligned concordantly >1 times ---- 845277 pairs aligned concordantly 0 times; of these: 345046 (40.82%) aligned discordantly 1 time ---- 500231 pairs aligned 0 times concordantly or discordantly; of these: 1000462 mates make up the pairs; of these: 777265 (77.69%) aligned 0 times 51429 (5.14%) aligned exactly 1 time 171768 (17.17%) aligned >1 times 88.71% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 122429 / 2915827 = 0.0420 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 08:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.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 08:39:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:39:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:39:54: 1000000 INFO @ Fri, 16 Oct 2020 08:40:00: 2000000 INFO @ Fri, 16 Oct 2020 08:40:05: 3000000 INFO @ Fri, 16 Oct 2020 08:40:11: 4000000 INFO @ Fri, 16 Oct 2020 08:40:16: 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 08:40:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.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 08:40:19: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:40:19: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:40:21: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:40:21: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:40:21: #1 total tags in treatment: 2492469 INFO @ Fri, 16 Oct 2020 08:40:21: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:40:21: #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 08:40:21: #1 tags after filtering in treatment: 1824573 INFO @ Fri, 16 Oct 2020 08:40:21: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 16 Oct 2020 08:40:21: #1 finished! INFO @ Fri, 16 Oct 2020 08:40:21: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:40:21: #2 number of paired peaks: 264 WARNING @ Fri, 16 Oct 2020 08:40:21: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Fri, 16 Oct 2020 08:40:21: start model_add_line... INFO @ Fri, 16 Oct 2020 08:40:21: start X-correlation... INFO @ Fri, 16 Oct 2020 08:40:21: end of X-cor INFO @ Fri, 16 Oct 2020 08:40:21: #2 finished! INFO @ Fri, 16 Oct 2020 08:40:21: #2 predicted fragment length is 172 bps INFO @ Fri, 16 Oct 2020 08:40:21: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 16 Oct 2020 08:40:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05_model.r WARNING @ Fri, 16 Oct 2020 08:40:21: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:40:21: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 16 Oct 2020 08:40:21: #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 08:40:21: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:40:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:40:25: 1000000 INFO @ Fri, 16 Oct 2020 08:40:26: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:40:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:40:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:40:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05_summits.bed INFO @ Fri, 16 Oct 2020 08:40:28: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1441 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:40:32: 2000000 INFO @ Fri, 16 Oct 2020 08:40:39: 3000000 INFO @ Fri, 16 Oct 2020 08:40:46: 4000000 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 08:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.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 08:40:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:40:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:40:53: 5000000 INFO @ Fri, 16 Oct 2020 08:40:54: 1000000 INFO @ Fri, 16 Oct 2020 08:40:58: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:40:58: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:40:58: #1 total tags in treatment: 2492469 INFO @ Fri, 16 Oct 2020 08:40:58: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:40:58: #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 08:40:58: #1 tags after filtering in treatment: 1824573 INFO @ Fri, 16 Oct 2020 08:40:58: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 16 Oct 2020 08:40:58: #1 finished! INFO @ Fri, 16 Oct 2020 08:40:58: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:40:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:40:58: #2 number of paired peaks: 264 WARNING @ Fri, 16 Oct 2020 08:40:58: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Fri, 16 Oct 2020 08:40:58: start model_add_line... INFO @ Fri, 16 Oct 2020 08:40:58: start X-correlation... INFO @ Fri, 16 Oct 2020 08:40:58: end of X-cor INFO @ Fri, 16 Oct 2020 08:40:58: #2 finished! INFO @ Fri, 16 Oct 2020 08:40:58: #2 predicted fragment length is 172 bps INFO @ Fri, 16 Oct 2020 08:40:58: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 16 Oct 2020 08:40:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10_model.r WARNING @ Fri, 16 Oct 2020 08:40:58: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:40:58: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 16 Oct 2020 08:40:58: #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 08:40:58: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:41:00: 2000000 INFO @ Fri, 16 Oct 2020 08:41:03: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10_summits.bed INFO @ Fri, 16 Oct 2020 08:41:05: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1048 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:41:05: 3000000 INFO @ Fri, 16 Oct 2020 08:41:11: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:41:16: 5000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:41:21: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:41:21: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:41:21: #1 total tags in treatment: 2492469 INFO @ Fri, 16 Oct 2020 08:41:21: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:41:21: #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 08:41:21: #1 tags after filtering in treatment: 1824573 INFO @ Fri, 16 Oct 2020 08:41:21: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 16 Oct 2020 08:41:21: #1 finished! INFO @ Fri, 16 Oct 2020 08:41:21: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:41:21: #2 number of paired peaks: 264 WARNING @ Fri, 16 Oct 2020 08:41:21: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Fri, 16 Oct 2020 08:41:21: start model_add_line... INFO @ Fri, 16 Oct 2020 08:41:21: start X-correlation... INFO @ Fri, 16 Oct 2020 08:41:21: end of X-cor INFO @ Fri, 16 Oct 2020 08:41:21: #2 finished! INFO @ Fri, 16 Oct 2020 08:41:21: #2 predicted fragment length is 172 bps INFO @ Fri, 16 Oct 2020 08:41:21: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 16 Oct 2020 08:41:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20_model.r WARNING @ Fri, 16 Oct 2020 08:41:21: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:41:21: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 16 Oct 2020 08:41:21: #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 08:41:21: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:41:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:41:26: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:41:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:41:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:41:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20_summits.bed INFO @ Fri, 16 Oct 2020 08:41:28: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (706 records, 4 fields): 3 millis CompletedMACS2peakCalling