Job ID = 6498602 SRX = SRX645111 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:31:11 prefetch.2.10.7: 1) Downloading 'SRR1505710'... 2020-06-26T00:31:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T01:06:44 prefetch.2.10.7: HTTPS download succeed 2020-06-26T01:06:44 prefetch.2.10.7: 1) 'SRR1505710' was downloaded successfully Read 158434566 spots for SRR1505710/SRR1505710.sra Written 158434566 spots for SRR1505710/SRR1505710.sra 2020-06-26T01:17:21 prefetch.2.10.7: 1) Downloading 'SRR1505711'... 2020-06-26T01:17:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T02:13:46 prefetch.2.10.7: HTTPS download succeed 2020-06-26T02:13:46 prefetch.2.10.7: 1) 'SRR1505711' was downloaded successfully Read 222238708 spots for SRR1505711/SRR1505711.sra Written 222238708 spots for SRR1505711/SRR1505711.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:12:08 380673274 reads; of these: 380673274 (100.00%) were unpaired; of these: 379082031 (99.58%) aligned 0 times 1295194 (0.34%) aligned exactly 1 time 296049 (0.08%) aligned >1 times 0.42% overall alignment rate Time searching: 01:12:10 Overall time: 01:12:10 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_rmdupse_core] 1058296 / 1591243 = 0.6651 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 12:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.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 12:55:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 12:55:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 12:55:53: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 12:55:53: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 12:55:53: #1 total tags in treatment: 532947 INFO @ Fri, 26 Jun 2020 12:55:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 12:55:53: #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 12:55:53: #1 tags after filtering in treatment: 532947 INFO @ Fri, 26 Jun 2020 12:55:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 12:55:53: #1 finished! INFO @ Fri, 26 Jun 2020 12:55:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 12:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 12:55:53: #2 number of paired peaks: 1106 INFO @ Fri, 26 Jun 2020 12:55:53: start model_add_line... INFO @ Fri, 26 Jun 2020 12:55:53: start X-correlation... INFO @ Fri, 26 Jun 2020 12:55:53: end of X-cor INFO @ Fri, 26 Jun 2020 12:55:53: #2 finished! INFO @ Fri, 26 Jun 2020 12:55:53: #2 predicted fragment length is 92 bps INFO @ Fri, 26 Jun 2020 12:55:53: #2 alternative fragment length(s) may be 92 bps INFO @ Fri, 26 Jun 2020 12:55:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.05_model.r WARNING @ Fri, 26 Jun 2020 12:55:53: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 12:55:53: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Fri, 26 Jun 2020 12:55:53: #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 12:55:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 12:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 12:55:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 12:55:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.05_peaks.xls INFO @ Fri, 26 Jun 2020 12:55:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 12:55:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.05_summits.bed INFO @ Fri, 26 Jun 2020 12:55:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1191 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 12:56:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.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 12:56:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 12:56:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 12:56:22: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 12:56:22: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 12:56:22: #1 total tags in treatment: 532947 INFO @ Fri, 26 Jun 2020 12:56:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 12:56:22: #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 12:56:22: #1 tags after filtering in treatment: 532947 INFO @ Fri, 26 Jun 2020 12:56:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 12:56:22: #1 finished! INFO @ Fri, 26 Jun 2020 12:56:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 12:56:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 12:56:22: #2 number of paired peaks: 1106 INFO @ Fri, 26 Jun 2020 12:56:22: start model_add_line... INFO @ Fri, 26 Jun 2020 12:56:22: start X-correlation... INFO @ Fri, 26 Jun 2020 12:56:22: end of X-cor INFO @ Fri, 26 Jun 2020 12:56:22: #2 finished! INFO @ Fri, 26 Jun 2020 12:56:22: #2 predicted fragment length is 92 bps INFO @ Fri, 26 Jun 2020 12:56:22: #2 alternative fragment length(s) may be 92 bps INFO @ Fri, 26 Jun 2020 12:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.10_model.r WARNING @ Fri, 26 Jun 2020 12:56:22: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 12:56:22: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Fri, 26 Jun 2020 12:56:22: #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 12:56:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 12:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 12:56:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 12:56:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.10_peaks.xls INFO @ Fri, 26 Jun 2020 12:56:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 12:56:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.10_summits.bed INFO @ Fri, 26 Jun 2020 12:56:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (668 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 12:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.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 12:56:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 12:56:48: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 12:56:51: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 12:56:51: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 12:56:51: #1 total tags in treatment: 532947 INFO @ Fri, 26 Jun 2020 12:56:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 12:56:51: #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 12:56:51: #1 tags after filtering in treatment: 532947 INFO @ Fri, 26 Jun 2020 12:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 12:56:51: #1 finished! INFO @ Fri, 26 Jun 2020 12:56:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 12:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 12:56:51: #2 number of paired peaks: 1106 INFO @ Fri, 26 Jun 2020 12:56:51: start model_add_line... INFO @ Fri, 26 Jun 2020 12:56:51: start X-correlation... INFO @ Fri, 26 Jun 2020 12:56:51: end of X-cor INFO @ Fri, 26 Jun 2020 12:56:51: #2 finished! INFO @ Fri, 26 Jun 2020 12:56:51: #2 predicted fragment length is 92 bps INFO @ Fri, 26 Jun 2020 12:56:51: #2 alternative fragment length(s) may be 92 bps INFO @ Fri, 26 Jun 2020 12:56:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.20_model.r WARNING @ Fri, 26 Jun 2020 12:56:51: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 12:56:51: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Fri, 26 Jun 2020 12:56:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 12:56:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 12:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 12:56:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 12:56:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.20_peaks.xls INFO @ Fri, 26 Jun 2020 12:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 12:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645111/SRX645111.20_summits.bed INFO @ Fri, 26 Jun 2020 12:56:53: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (278 records, 4 fields): 1 millis CompletedMACS2peakCalling