Job ID = 6498683 SRX = SRX699106 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:52:06 prefetch.2.10.7: 1) Downloading 'SRR1573143'... 2020-06-25T23:52:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:53:55 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:53:56 prefetch.2.10.7: 'SRR1573143' is valid 2020-06-25T23:53:56 prefetch.2.10.7: 1) 'SRR1573143' was downloaded successfully Read 3455643 spots for SRR1573143/SRR1573143.sra Written 3455643 spots for SRR1573143/SRR1573143.sra 2020-06-25T23:54:32 prefetch.2.10.7: 1) Downloading 'SRR1573144'... 2020-06-25T23:54:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:56:45 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:56:46 prefetch.2.10.7: 'SRR1573144' is valid 2020-06-25T23:56:46 prefetch.2.10.7: 1) 'SRR1573144' was downloaded successfully Read 3419032 spots for SRR1573144/SRR1573144.sra Written 3419032 spots for SRR1573144/SRR1573144.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: 00:21:52 6874675 reads; of these: 6874675 (100.00%) were paired; of these: 455189 (6.62%) aligned concordantly 0 times 5044934 (73.38%) aligned concordantly exactly 1 time 1374552 (19.99%) aligned concordantly >1 times ---- 455189 pairs aligned concordantly 0 times; of these: 79492 (17.46%) aligned discordantly 1 time ---- 375697 pairs aligned 0 times concordantly or discordantly; of these: 751394 mates make up the pairs; of these: 342213 (45.54%) aligned 0 times 188803 (25.13%) aligned exactly 1 time 220378 (29.33%) aligned >1 times 97.51% overall alignment rate Time searching: 00:21:52 Overall time: 00:21:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 935197 / 6470374 = 0.1445 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, 26 Jun 2020 09:25:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 26 Jun 2020 09:25:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:25:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:25:50: 1000000 INFO @ Fri, 26 Jun 2020 09:25:57: 2000000 INFO @ Fri, 26 Jun 2020 09:26:04: 3000000 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, 26 Jun 2020 09:26:11: 4000000 INFO @ Fri, 26 Jun 2020 09:26:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 26 Jun 2020 09:26:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:19: 5000000 INFO @ Fri, 26 Jun 2020 09:26:20: 1000000 INFO @ Fri, 26 Jun 2020 09:26:27: 6000000 INFO @ Fri, 26 Jun 2020 09:26:27: 2000000 INFO @ Fri, 26 Jun 2020 09:26:34: 7000000 INFO @ Fri, 26 Jun 2020 09:26:34: 3000000 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, 26 Jun 2020 09:26:42: 4000000 INFO @ Fri, 26 Jun 2020 09:26:42: 8000000 INFO @ Fri, 26 Jun 2020 09:26:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 26 Jun 2020 09:26:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:50: 5000000 INFO @ Fri, 26 Jun 2020 09:26:50: 9000000 INFO @ Fri, 26 Jun 2020 09:26:50: 1000000 INFO @ Fri, 26 Jun 2020 09:26:57: 6000000 INFO @ Fri, 26 Jun 2020 09:26:57: 2000000 INFO @ Fri, 26 Jun 2020 09:26:58: 10000000 INFO @ Fri, 26 Jun 2020 09:27:05: 7000000 INFO @ Fri, 26 Jun 2020 09:27:06: 3000000 INFO @ Fri, 26 Jun 2020 09:27:06: 11000000 INFO @ Fri, 26 Jun 2020 09:27:10: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:27:10: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:27:10: #1 total tags in treatment: 5486621 INFO @ Fri, 26 Jun 2020 09:27:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:27:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:27:10: #1 tags after filtering in treatment: 4835887 INFO @ Fri, 26 Jun 2020 09:27:10: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 09:27:10: #1 finished! INFO @ Fri, 26 Jun 2020 09:27:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:27:11: #2 number of paired peaks: 2423 INFO @ Fri, 26 Jun 2020 09:27:11: start model_add_line... INFO @ Fri, 26 Jun 2020 09:27:11: start X-correlation... INFO @ Fri, 26 Jun 2020 09:27:11: end of X-cor INFO @ Fri, 26 Jun 2020 09:27:11: #2 finished! INFO @ Fri, 26 Jun 2020 09:27:11: #2 predicted fragment length is 163 bps INFO @ Fri, 26 Jun 2020 09:27:11: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 26 Jun 2020 09:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.05_model.r WARNING @ Fri, 26 Jun 2020 09:27:11: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:27:11: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Fri, 26 Jun 2020 09:27:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:27:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:27:13: 8000000 INFO @ Fri, 26 Jun 2020 09:27:13: 4000000 INFO @ Fri, 26 Jun 2020 09:27:21: 9000000 INFO @ Fri, 26 Jun 2020 09:27:22: 5000000 INFO @ Fri, 26 Jun 2020 09:27:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:27:29: 10000000 INFO @ Fri, 26 Jun 2020 09:27:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:27:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:27:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.05_summits.bed INFO @ Fri, 26 Jun 2020 09:27:30: Done! INFO @ Fri, 26 Jun 2020 09:27:30: 6000000 pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13008 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:27:37: 11000000 INFO @ Fri, 26 Jun 2020 09:27:38: 7000000 INFO @ Fri, 26 Jun 2020 09:27:41: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:27:41: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:27:41: #1 total tags in treatment: 5486621 INFO @ Fri, 26 Jun 2020 09:27:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:27:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:27:41: #1 tags after filtering in treatment: 4835887 INFO @ Fri, 26 Jun 2020 09:27:41: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 09:27:41: #1 finished! INFO @ Fri, 26 Jun 2020 09:27:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:27:41: #2 number of paired peaks: 2423 INFO @ Fri, 26 Jun 2020 09:27:41: start model_add_line... INFO @ Fri, 26 Jun 2020 09:27:41: start X-correlation... INFO @ Fri, 26 Jun 2020 09:27:42: end of X-cor INFO @ Fri, 26 Jun 2020 09:27:42: #2 finished! INFO @ Fri, 26 Jun 2020 09:27:42: #2 predicted fragment length is 163 bps INFO @ Fri, 26 Jun 2020 09:27:42: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 26 Jun 2020 09:27:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.10_model.r WARNING @ Fri, 26 Jun 2020 09:27:42: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:27:42: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Fri, 26 Jun 2020 09:27:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:27:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:27:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:27:46: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:27:53: 9000000 INFO @ Fri, 26 Jun 2020 09:27:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:28:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:28:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:28:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.10_summits.bed INFO @ Fri, 26 Jun 2020 09:28:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5042 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:28:01: 10000000 INFO @ Fri, 26 Jun 2020 09:28:09: 11000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:28:13: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:28:13: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:28:13: #1 total tags in treatment: 5486621 INFO @ Fri, 26 Jun 2020 09:28:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:28:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:28:13: #1 tags after filtering in treatment: 4835887 INFO @ Fri, 26 Jun 2020 09:28:13: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 09:28:13: #1 finished! INFO @ Fri, 26 Jun 2020 09:28:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:28:13: #2 number of paired peaks: 2423 INFO @ Fri, 26 Jun 2020 09:28:13: start model_add_line... INFO @ Fri, 26 Jun 2020 09:28:13: start X-correlation... INFO @ Fri, 26 Jun 2020 09:28:13: end of X-cor INFO @ Fri, 26 Jun 2020 09:28:13: #2 finished! INFO @ Fri, 26 Jun 2020 09:28:13: #2 predicted fragment length is 163 bps INFO @ Fri, 26 Jun 2020 09:28:13: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 26 Jun 2020 09:28:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.20_model.r WARNING @ Fri, 26 Jun 2020 09:28:13: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:28:13: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Fri, 26 Jun 2020 09:28:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:28:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:28:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:28:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699106/SRX699106.20_summits.bed INFO @ Fri, 26 Jun 2020 09:28:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1460 records, 4 fields): 3 millis CompletedMACS2peakCalling