Job ID = 10223888 SRX = ERX4439629 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:36:26 prefetch.2.10.7: 1) Downloading 'ERR4501558'... 2020-10-15T23:36:26 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:37:08 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:37:08 prefetch.2.10.7: 'ERR4501558' is valid 2020-10-15T23:37:08 prefetch.2.10.7: 1) 'ERR4501558' was downloaded successfully 2020-10-15T23:37:36 prefetch.2.10.7: 'ERR4501558' has 5 unresolved dependencies 2020-10-15T23:37:36 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:37:36 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:37:44 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:37:44 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:37:44 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:37:44 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:37:56 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:37:56 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:37:56 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:37:56 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:38:05 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:38:05 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:38:05 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:38:05 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:38:17 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:38:17 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:38:17 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:38:17 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:38:27 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:38:27 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3901398 spots for ERR4501558/ERR4501558.sra Written 3901398 spots for ERR4501558/ERR4501558.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: 00:02:43 3901398 reads; of these: 3901398 (100.00%) were paired; of these: 903881 (23.17%) aligned concordantly 0 times 2659256 (68.16%) aligned concordantly exactly 1 time 338261 (8.67%) aligned concordantly >1 times ---- 903881 pairs aligned concordantly 0 times; of these: 395121 (43.71%) aligned discordantly 1 time ---- 508760 pairs aligned 0 times concordantly or discordantly; of these: 1017520 mates make up the pairs; of these: 860394 (84.56%) aligned 0 times 56483 (5.55%) aligned exactly 1 time 100643 (9.89%) aligned >1 times 88.97% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 84875 / 3365954 = 0.0252 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 08:45:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.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 08:45:12: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:45:12: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:45:19: 1000000 INFO @ Fri, 16 Oct 2020 08:45:26: 2000000 INFO @ Fri, 16 Oct 2020 08:45:33: 3000000 INFO @ Fri, 16 Oct 2020 08:45:40: 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 08:45:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.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 08:45:42: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:45:42: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:45:47: 5000000 INFO @ Fri, 16 Oct 2020 08:45:51: 1000000 INFO @ Fri, 16 Oct 2020 08:45:54: 6000000 INFO @ Fri, 16 Oct 2020 08:45:59: 2000000 INFO @ Fri, 16 Oct 2020 08:46:00: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:46:00: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:46:00: #1 total tags in treatment: 2933070 INFO @ Fri, 16 Oct 2020 08:46:00: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:46:00: #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 08:46:00: #1 tags after filtering in treatment: 2161605 INFO @ Fri, 16 Oct 2020 08:46:00: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 16 Oct 2020 08:46:00: #1 finished! INFO @ Fri, 16 Oct 2020 08:46:00: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:46:00: #2 number of paired peaks: 161 WARNING @ Fri, 16 Oct 2020 08:46:00: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Fri, 16 Oct 2020 08:46:00: start model_add_line... INFO @ Fri, 16 Oct 2020 08:46:00: start X-correlation... INFO @ Fri, 16 Oct 2020 08:46:00: end of X-cor INFO @ Fri, 16 Oct 2020 08:46:00: #2 finished! INFO @ Fri, 16 Oct 2020 08:46:00: #2 predicted fragment length is 193 bps INFO @ Fri, 16 Oct 2020 08:46:00: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 16 Oct 2020 08:46:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.05_model.r WARNING @ Fri, 16 Oct 2020 08:46:00: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:46:00: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Fri, 16 Oct 2020 08:46:00: #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 08:46:00: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:46:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:46:06: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:46:08: 3000000 INFO @ Fri, 16 Oct 2020 08:46:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:46:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:46:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.05_summits.bed INFO @ Fri, 16 Oct 2020 08:46:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2851 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 08:46:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.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 08:46:12: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:46:12: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:46:16: 4000000 INFO @ Fri, 16 Oct 2020 08:46:20: 1000000 INFO @ Fri, 16 Oct 2020 08:46:25: 5000000 INFO @ Fri, 16 Oct 2020 08:46:29: 2000000 INFO @ Fri, 16 Oct 2020 08:46:33: 6000000 INFO @ Fri, 16 Oct 2020 08:46:37: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:46:40: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:46:40: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:46:40: #1 total tags in treatment: 2933070 INFO @ Fri, 16 Oct 2020 08:46:40: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:46:40: #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 08:46:40: #1 tags after filtering in treatment: 2161605 INFO @ Fri, 16 Oct 2020 08:46:40: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 16 Oct 2020 08:46:40: #1 finished! INFO @ Fri, 16 Oct 2020 08:46:40: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:46:40: #2 number of paired peaks: 161 WARNING @ Fri, 16 Oct 2020 08:46:40: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Fri, 16 Oct 2020 08:46:40: start model_add_line... INFO @ Fri, 16 Oct 2020 08:46:40: start X-correlation... INFO @ Fri, 16 Oct 2020 08:46:40: end of X-cor INFO @ Fri, 16 Oct 2020 08:46:40: #2 finished! INFO @ Fri, 16 Oct 2020 08:46:40: #2 predicted fragment length is 193 bps INFO @ Fri, 16 Oct 2020 08:46:40: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 16 Oct 2020 08:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.10_model.r WARNING @ Fri, 16 Oct 2020 08:46:40: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:46:40: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Fri, 16 Oct 2020 08:46:40: #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 08:46:40: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:46:46: 4000000 INFO @ Fri, 16 Oct 2020 08:46:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:46:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:46:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:46:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.10_summits.bed INFO @ Fri, 16 Oct 2020 08:46:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2092 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:46:53: 5000000 INFO @ Fri, 16 Oct 2020 08:47:01: 6000000 INFO @ Fri, 16 Oct 2020 08:47:07: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:47:07: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:47:07: #1 total tags in treatment: 2933070 INFO @ Fri, 16 Oct 2020 08:47:07: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:47:07: #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 08:47:08: #1 tags after filtering in treatment: 2161605 INFO @ Fri, 16 Oct 2020 08:47:08: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 16 Oct 2020 08:47:08: #1 finished! INFO @ Fri, 16 Oct 2020 08:47:08: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:47:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:47:08: #2 number of paired peaks: 161 WARNING @ Fri, 16 Oct 2020 08:47:08: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Fri, 16 Oct 2020 08:47:08: start model_add_line... INFO @ Fri, 16 Oct 2020 08:47:08: start X-correlation... INFO @ Fri, 16 Oct 2020 08:47:08: end of X-cor INFO @ Fri, 16 Oct 2020 08:47:08: #2 finished! INFO @ Fri, 16 Oct 2020 08:47:08: #2 predicted fragment length is 193 bps INFO @ Fri, 16 Oct 2020 08:47:08: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 16 Oct 2020 08:47:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.20_model.r WARNING @ Fri, 16 Oct 2020 08:47:08: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:47:08: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Fri, 16 Oct 2020 08:47:08: #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 08:47:08: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:47:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:47:14: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:47:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439629/ERX4439629.20_summits.bed INFO @ Fri, 16 Oct 2020 08:47:16: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1390 records, 4 fields): 3 millis CompletedMACS2peakCalling