Job ID = 6455968 SRX = SRX3088629 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:29:51 prefetch.2.10.7: 1) Downloading 'SRR5928310'... 2020-06-21T10:29:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:37:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:37:17 prefetch.2.10.7: 1) 'SRR5928310' was downloaded successfully 2020-06-21T10:37:17 prefetch.2.10.7: 'SRR5928310' has 0 unresolved dependencies Read 48381350 spots for SRR5928310/SRR5928310.sra Written 48381350 spots for SRR5928310/SRR5928310.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: 00:08:59 48381350 reads; of these: 48381350 (100.00%) were unpaired; of these: 20107282 (41.56%) aligned 0 times 20222125 (41.80%) aligned exactly 1 time 8051943 (16.64%) aligned >1 times 58.44% overall alignment rate Time searching: 00:08:59 Overall time: 00:08:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 16535808 / 28274068 = 0.5848 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 @ Sun, 21 Jun 2020 19:54:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.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 @ Sun, 21 Jun 2020 19:54:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:38: 1000000 INFO @ Sun, 21 Jun 2020 19:54:44: 2000000 INFO @ Sun, 21 Jun 2020 19:54:50: 3000000 INFO @ Sun, 21 Jun 2020 19:54:56: 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 @ Sun, 21 Jun 2020 19:55:02: 5000000 INFO @ Sun, 21 Jun 2020 19:55:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.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 @ Sun, 21 Jun 2020 19:55:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:55:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:55:08: 6000000 INFO @ Sun, 21 Jun 2020 19:55:10: 1000000 INFO @ Sun, 21 Jun 2020 19:55:15: 7000000 INFO @ Sun, 21 Jun 2020 19:55:17: 2000000 INFO @ Sun, 21 Jun 2020 19:55:21: 8000000 INFO @ Sun, 21 Jun 2020 19:55:24: 3000000 INFO @ Sun, 21 Jun 2020 19:55:28: 9000000 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 @ Sun, 21 Jun 2020 19:55:31: 4000000 INFO @ Sun, 21 Jun 2020 19:55:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.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 @ Sun, 21 Jun 2020 19:55:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:55:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:55:35: 10000000 INFO @ Sun, 21 Jun 2020 19:55:38: 5000000 INFO @ Sun, 21 Jun 2020 19:55:39: 1000000 INFO @ Sun, 21 Jun 2020 19:55:42: 11000000 INFO @ Sun, 21 Jun 2020 19:55:45: 6000000 INFO @ Sun, 21 Jun 2020 19:55:46: 2000000 INFO @ Sun, 21 Jun 2020 19:55:47: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 19:55:47: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 19:55:47: #1 total tags in treatment: 11738260 INFO @ Sun, 21 Jun 2020 19:55:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:55:48: #1 tags after filtering in treatment: 11738254 INFO @ Sun, 21 Jun 2020 19:55:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:49: #2 number of paired peaks: 1175 INFO @ Sun, 21 Jun 2020 19:55:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:49: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:55:49: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.05_model.r WARNING @ Sun, 21 Jun 2020 19:55:49: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:55:49: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:55:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:55:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:52: 7000000 INFO @ Sun, 21 Jun 2020 19:55:53: 3000000 INFO @ Sun, 21 Jun 2020 19:55:59: 8000000 INFO @ Sun, 21 Jun 2020 19:56:00: 4000000 INFO @ Sun, 21 Jun 2020 19:56:06: 5000000 INFO @ Sun, 21 Jun 2020 19:56:07: 9000000 INFO @ Sun, 21 Jun 2020 19:56:13: 6000000 INFO @ Sun, 21 Jun 2020 19:56:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:14: 10000000 INFO @ Sun, 21 Jun 2020 19:56:20: 7000000 INFO @ Sun, 21 Jun 2020 19:56:22: 11000000 INFO @ Sun, 21 Jun 2020 19:56:26: 8000000 INFO @ Sun, 21 Jun 2020 19:56:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.05_summits.bed INFO @ Sun, 21 Jun 2020 19:56:26: Done! pass1 - making usageList (633 chroms): 1 millis pass2 - checking and writing primary data (4646 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:56:27: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 19:56:27: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 19:56:27: #1 total tags in treatment: 11738260 INFO @ Sun, 21 Jun 2020 19:56:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:56:28: #1 tags after filtering in treatment: 11738254 INFO @ Sun, 21 Jun 2020 19:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:28: #2 number of paired peaks: 1175 INFO @ Sun, 21 Jun 2020 19:56:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:29: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:56:29: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.10_model.r WARNING @ Sun, 21 Jun 2020 19:56:29: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:56:29: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:56:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:56:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:33: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:56:39: 10000000 INFO @ Sun, 21 Jun 2020 19:56:45: 11000000 INFO @ Sun, 21 Jun 2020 19:56:50: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 19:56:50: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 19:56:50: #1 total tags in treatment: 11738260 INFO @ Sun, 21 Jun 2020 19:56:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:56:50: #1 tags after filtering in treatment: 11738254 INFO @ Sun, 21 Jun 2020 19:56:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:51: #2 number of paired peaks: 1175 INFO @ Sun, 21 Jun 2020 19:56:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:51: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:56:51: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:56:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.20_model.r WARNING @ Sun, 21 Jun 2020 19:56:51: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:56:51: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:56:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:56:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:57:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.10_summits.bed INFO @ Sun, 21 Jun 2020 19:57:04: Done! pass1 - making usageList (538 chroms): 1 millis pass2 - checking and writing primary data (2393 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:57:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:57:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3088629/SRX3088629.20_summits.bed INFO @ Sun, 21 Jun 2020 19:57:28: Done! pass1 - making usageList (466 chroms): 1 millis pass2 - checking and writing primary data (1773 records, 4 fields): 16 millis CompletedMACS2peakCalling