Job ID = 6498689 SRX = SRX699114 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:47:23 prefetch.2.10.7: 1) Downloading 'SRR1573159'... 2020-06-26T00:47:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:48:51 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:48:52 prefetch.2.10.7: 'SRR1573159' is valid 2020-06-26T00:48:52 prefetch.2.10.7: 1) 'SRR1573159' was downloaded successfully Read 3741296 spots for SRR1573159/SRR1573159.sra Written 3741296 spots for SRR1573159/SRR1573159.sra 2020-06-26T00:49:34 prefetch.2.10.7: 1) Downloading 'SRR1573160'... 2020-06-26T00:49:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:51:12 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:51:13 prefetch.2.10.7: 'SRR1573160' is valid 2020-06-26T00:51:13 prefetch.2.10.7: 1) 'SRR1573160' was downloaded successfully Read 3808556 spots for SRR1573160/SRR1573160.sra Written 3808556 spots for SRR1573160/SRR1573160.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: 00:15:41 7549852 reads; of these: 7549852 (100.00%) were paired; of these: 393027 (5.21%) aligned concordantly 0 times 6483566 (85.88%) aligned concordantly exactly 1 time 673259 (8.92%) aligned concordantly >1 times ---- 393027 pairs aligned concordantly 0 times; of these: 80369 (20.45%) aligned discordantly 1 time ---- 312658 pairs aligned 0 times concordantly or discordantly; of these: 625316 mates make up the pairs; of these: 331341 (52.99%) aligned 0 times 202203 (32.34%) aligned exactly 1 time 91772 (14.68%) aligned >1 times 97.81% overall alignment rate Time searching: 00:15:41 Overall time: 00:15:41 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] 506308 / 7224989 = 0.0701 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 10:15:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.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 10:15:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:15:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:15:30: 1000000 INFO @ Fri, 26 Jun 2020 10:15:40: 2000000 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 10:15:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.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 10:15:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:15:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:15:51: 3000000 INFO @ Fri, 26 Jun 2020 10:16:01: 1000000 INFO @ Fri, 26 Jun 2020 10:16:03: 4000000 INFO @ Fri, 26 Jun 2020 10:16:13: 2000000 INFO @ Fri, 26 Jun 2020 10:16:15: 5000000 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 10:16:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.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 10:16:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:16:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:16:25: 3000000 INFO @ Fri, 26 Jun 2020 10:16:27: 6000000 INFO @ Fri, 26 Jun 2020 10:16:31: 1000000 INFO @ Fri, 26 Jun 2020 10:16:37: 4000000 INFO @ Fri, 26 Jun 2020 10:16:40: 7000000 INFO @ Fri, 26 Jun 2020 10:16:44: 2000000 INFO @ Fri, 26 Jun 2020 10:16:50: 5000000 INFO @ Fri, 26 Jun 2020 10:16:53: 8000000 INFO @ Fri, 26 Jun 2020 10:16:56: 3000000 INFO @ Fri, 26 Jun 2020 10:17:03: 6000000 INFO @ Fri, 26 Jun 2020 10:17:05: 9000000 INFO @ Fri, 26 Jun 2020 10:17:08: 4000000 INFO @ Fri, 26 Jun 2020 10:17:15: 7000000 INFO @ Fri, 26 Jun 2020 10:17:18: 10000000 INFO @ Fri, 26 Jun 2020 10:17:20: 5000000 INFO @ Fri, 26 Jun 2020 10:17:28: 8000000 INFO @ Fri, 26 Jun 2020 10:17:30: 11000000 INFO @ Fri, 26 Jun 2020 10:17:33: 6000000 INFO @ Fri, 26 Jun 2020 10:17:42: 9000000 INFO @ Fri, 26 Jun 2020 10:17:44: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:17:46: 7000000 INFO @ Fri, 26 Jun 2020 10:17:55: 10000000 INFO @ Fri, 26 Jun 2020 10:17:57: 13000000 INFO @ Fri, 26 Jun 2020 10:18:00: 8000000 INFO @ Fri, 26 Jun 2020 10:18:07: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 10:18:07: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 10:18:07: #1 total tags in treatment: 6654707 INFO @ Fri, 26 Jun 2020 10:18:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:18:07: #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 10:18:08: #1 tags after filtering in treatment: 6219065 INFO @ Fri, 26 Jun 2020 10:18:08: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 10:18:08: #1 finished! INFO @ Fri, 26 Jun 2020 10:18:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:18:08: #2 number of paired peaks: 1389 INFO @ Fri, 26 Jun 2020 10:18:08: start model_add_line... INFO @ Fri, 26 Jun 2020 10:18:08: start X-correlation... INFO @ Fri, 26 Jun 2020 10:18:08: end of X-cor INFO @ Fri, 26 Jun 2020 10:18:08: #2 finished! INFO @ Fri, 26 Jun 2020 10:18:08: #2 predicted fragment length is 185 bps INFO @ Fri, 26 Jun 2020 10:18:08: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 26 Jun 2020 10:18:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.05_model.r WARNING @ Fri, 26 Jun 2020 10:18:08: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:18:08: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Fri, 26 Jun 2020 10:18:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 10:18:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:18:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:18:08: 11000000 INFO @ Fri, 26 Jun 2020 10:18:13: 9000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:18:21: 12000000 INFO @ Fri, 26 Jun 2020 10:18:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:18:26: 10000000 INFO @ Fri, 26 Jun 2020 10:18:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:18:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:18:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.05_summits.bed INFO @ Fri, 26 Jun 2020 10:18:33: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (15998 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:18:34: 13000000 INFO @ Fri, 26 Jun 2020 10:18:39: 11000000 INFO @ Fri, 26 Jun 2020 10:18:44: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 10:18:44: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 10:18:44: #1 total tags in treatment: 6654707 INFO @ Fri, 26 Jun 2020 10:18:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:18:44: #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 10:18:44: #1 tags after filtering in treatment: 6219065 INFO @ Fri, 26 Jun 2020 10:18:44: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 10:18:44: #1 finished! INFO @ Fri, 26 Jun 2020 10:18:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:18:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:18:44: #2 number of paired peaks: 1389 INFO @ Fri, 26 Jun 2020 10:18:44: start model_add_line... INFO @ Fri, 26 Jun 2020 10:18:45: start X-correlation... INFO @ Fri, 26 Jun 2020 10:18:45: end of X-cor INFO @ Fri, 26 Jun 2020 10:18:45: #2 finished! INFO @ Fri, 26 Jun 2020 10:18:45: #2 predicted fragment length is 185 bps INFO @ Fri, 26 Jun 2020 10:18:45: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 26 Jun 2020 10:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.10_model.r WARNING @ Fri, 26 Jun 2020 10:18:45: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:18:45: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Fri, 26 Jun 2020 10:18:45: #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 10:18:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:18:51: 12000000 INFO @ Fri, 26 Jun 2020 10:19:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:19:03: 13000000 INFO @ Fri, 26 Jun 2020 10:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.10_summits.bed INFO @ Fri, 26 Jun 2020 10:19:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6011 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:19:12: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 10:19:12: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 10:19:12: #1 total tags in treatment: 6654707 INFO @ Fri, 26 Jun 2020 10:19:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:19:12: #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 10:19:12: #1 tags after filtering in treatment: 6219065 INFO @ Fri, 26 Jun 2020 10:19:12: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 10:19:12: #1 finished! INFO @ Fri, 26 Jun 2020 10:19:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:19:12: #2 number of paired peaks: 1389 INFO @ Fri, 26 Jun 2020 10:19:12: start model_add_line... INFO @ Fri, 26 Jun 2020 10:19:12: start X-correlation... INFO @ Fri, 26 Jun 2020 10:19:12: end of X-cor INFO @ Fri, 26 Jun 2020 10:19:12: #2 finished! INFO @ Fri, 26 Jun 2020 10:19:12: #2 predicted fragment length is 185 bps INFO @ Fri, 26 Jun 2020 10:19:12: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 26 Jun 2020 10:19:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.20_model.r WARNING @ Fri, 26 Jun 2020 10:19:12: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:19:12: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Fri, 26 Jun 2020 10:19:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 10:19:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:19:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:19:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:19:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:19:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:19:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699114/SRX699114.20_summits.bed INFO @ Fri, 26 Jun 2020 10:19:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1085 records, 4 fields): 43 millis CompletedMACS2peakCalling