Job ID = 6454147 SRX = SRX1840068 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:54:04 prefetch.2.10.7: 1) Downloading 'SRR3661294'... 2020-06-21T08:54:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:58:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:58:58 prefetch.2.10.7: 1) 'SRR3661294' was downloaded successfully Read 18948240 spots for SRR3661294/SRR3661294.sra Written 18948240 spots for SRR3661294/SRR3661294.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: 00:11:26 18948240 reads; of these: 18948240 (100.00%) were unpaired; of these: 2881725 (15.21%) aligned 0 times 11518341 (60.79%) aligned exactly 1 time 4548174 (24.00%) aligned >1 times 84.79% overall alignment rate Time searching: 00:11:26 Overall time: 00:11:26 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 8 files... [bam_rmdupse_core] 12320897 / 16066515 = 0.7669 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 18:16:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.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 18:16:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:53: 1000000 INFO @ Sun, 21 Jun 2020 18:17:00: 2000000 INFO @ Sun, 21 Jun 2020 18:17:08: 3000000 INFO @ Sun, 21 Jun 2020 18:17:13: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:17:13: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:17:13: #1 total tags in treatment: 3745618 INFO @ Sun, 21 Jun 2020 18:17:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:13: #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 18:17:13: #1 tags after filtering in treatment: 3745592 INFO @ Sun, 21 Jun 2020 18:17:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:14: #2 number of paired peaks: 2329 INFO @ Sun, 21 Jun 2020 18:17:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:14: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 18:17:14: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 21 Jun 2020 18:17:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.05_model.r WARNING @ Sun, 21 Jun 2020 18:17:14: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:17:14: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sun, 21 Jun 2020 18:17:14: #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 18:17:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:14: #3 Pre-compute pvalue-qvalue table... 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 18:17:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.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 18:17:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:23: 1000000 INFO @ Sun, 21 Jun 2020 18:17:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.05_summits.bed INFO @ Sun, 21 Jun 2020 18:17:27: Done! pass1 - making usageList (830 chroms): 1 millis pass2 - checking and writing primary data (2489 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:17:30: 2000000 INFO @ Sun, 21 Jun 2020 18:17:37: 3000000 INFO @ Sun, 21 Jun 2020 18:17:43: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:17:43: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:17:43: #1 total tags in treatment: 3745618 INFO @ Sun, 21 Jun 2020 18:17:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:43: #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 18:17:43: #1 tags after filtering in treatment: 3745592 INFO @ Sun, 21 Jun 2020 18:17:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:43: #2 number of paired peaks: 2329 INFO @ Sun, 21 Jun 2020 18:17:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:43: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 18:17:43: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 21 Jun 2020 18:17:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.10_model.r WARNING @ Sun, 21 Jun 2020 18:17:43: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:17:43: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sun, 21 Jun 2020 18:17:43: #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 18:17:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:43: #3 Pre-compute pvalue-qvalue table... 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 18:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.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 18:17:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:55: 1000000 INFO @ Sun, 21 Jun 2020 18:17:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.10_summits.bed INFO @ Sun, 21 Jun 2020 18:17:56: Done! pass1 - making usageList (652 chroms): 1 millis pass2 - checking and writing primary data (1508 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:18:04: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:18:13: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:18:20: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:18:20: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:18:20: #1 total tags in treatment: 3745618 INFO @ Sun, 21 Jun 2020 18:18:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:20: #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 18:18:20: #1 tags after filtering in treatment: 3745592 INFO @ Sun, 21 Jun 2020 18:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:20: #2 number of paired peaks: 2329 INFO @ Sun, 21 Jun 2020 18:18:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:20: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 18:18:20: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 21 Jun 2020 18:18:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.20_model.r WARNING @ Sun, 21 Jun 2020 18:18:20: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:18:20: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sun, 21 Jun 2020 18:18:20: #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 18:18:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:18:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:18:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840068/SRX1840068.20_summits.bed INFO @ Sun, 21 Jun 2020 18:18:34: Done! pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (980 records, 4 fields): 15 millis CompletedMACS2peakCalling