Job ID = 6457895 SRX = SRX482858 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:57:48 prefetch.2.10.7: 1) Downloading 'SRR1185444'... 2020-06-21T11:57:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:11:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:11:06 prefetch.2.10.7: 1) 'SRR1185444' was downloaded successfully Read 32907349 spots for SRR1185444/SRR1185444.sra Written 32907349 spots for SRR1185444/SRR1185444.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: 00:10:57 32907349 reads; of these: 32907349 (100.00%) were unpaired; of these: 20661292 (62.79%) aligned 0 times 10624655 (32.29%) aligned exactly 1 time 1621402 (4.93%) aligned >1 times 37.21% overall alignment rate Time searching: 00:10:57 Overall time: 00:10:57 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] 9147183 / 12246057 = 0.7469 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 21:28:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.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 21:28:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:08: 1000000 INFO @ Sun, 21 Jun 2020 21:28:15: 2000000 INFO @ Sun, 21 Jun 2020 21:28:23: 3000000 INFO @ Sun, 21 Jun 2020 21:28:24: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 21:28:24: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 21:28:24: #1 total tags in treatment: 3098874 INFO @ Sun, 21 Jun 2020 21:28:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:24: #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 21:28:25: #1 tags after filtering in treatment: 3098595 INFO @ Sun, 21 Jun 2020 21:28:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:25: #2 number of paired peaks: 4248 INFO @ Sun, 21 Jun 2020 21:28:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:25: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 21:28:25: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 21:28:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.05_model.r WARNING @ Sun, 21 Jun 2020 21:28:25: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:28:25: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 21:28:25: #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 21:28:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:25: #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 21:28:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.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 21:28:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:28:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:28:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.05_summits.bed INFO @ Sun, 21 Jun 2020 21:28:36: Done! INFO @ Sun, 21 Jun 2020 21:28:37: 1000000 pass1 - making usageList (314 chroms): 2 millis pass2 - checking and writing primary data (7098 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:28:43: 2000000 INFO @ Sun, 21 Jun 2020 21:28:50: 3000000 INFO @ Sun, 21 Jun 2020 21:28:50: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 21:28:50: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 21:28:50: #1 total tags in treatment: 3098874 INFO @ Sun, 21 Jun 2020 21:28:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:50: #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 21:28:51: #1 tags after filtering in treatment: 3098595 INFO @ Sun, 21 Jun 2020 21:28:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:51: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:51: #2 number of paired peaks: 4248 INFO @ Sun, 21 Jun 2020 21:28:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:51: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 21:28:51: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 21:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.10_model.r WARNING @ Sun, 21 Jun 2020 21:28:51: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:28:51: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 21:28:51: #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 21:28:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:51: #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 21:28:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.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 21:29:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.10_summits.bed INFO @ Sun, 21 Jun 2020 21:29:03: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (3923 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:29:07: 1000000 INFO @ Sun, 21 Jun 2020 21:29:13: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:29:19: 3000000 INFO @ Sun, 21 Jun 2020 21:29:20: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 21:29:20: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 21:29:20: #1 total tags in treatment: 3098874 INFO @ Sun, 21 Jun 2020 21:29:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:20: #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 21:29:21: #1 tags after filtering in treatment: 3098595 INFO @ Sun, 21 Jun 2020 21:29:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:21: #2 number of paired peaks: 4248 INFO @ Sun, 21 Jun 2020 21:29:21: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:21: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 21:29:21: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 21:29:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.20_model.r WARNING @ Sun, 21 Jun 2020 21:29:21: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:21: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 21:29:21: #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 21:29:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:29:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX482858/SRX482858.20_summits.bed INFO @ Sun, 21 Jun 2020 21:29:32: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (1910 records, 4 fields): 5 millis CompletedMACS2peakCalling