Job ID = 6453118 SRX = SRX1032417 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:02:08 prefetch.2.10.7: 1) Downloading 'SRR2031918'... 2020-06-21T08:02:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:02:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:02:42 prefetch.2.10.7: 'SRR2031918' is valid 2020-06-21T08:02:42 prefetch.2.10.7: 1) 'SRR2031918' was downloaded successfully Read 3186803 spots for SRR2031918/SRR2031918.sra Written 3186803 spots for SRR2031918/SRR2031918.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: 00:00:47 3186803 reads; of these: 3186803 (100.00%) were unpaired; of these: 154442 (4.85%) aligned 0 times 1967298 (61.73%) aligned exactly 1 time 1065063 (33.42%) aligned >1 times 95.15% overall alignment rate Time searching: 00:00:47 Overall time: 00:00:47 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_rmdupse_core] 916404 / 3032361 = 0.3022 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 17:04:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.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 17:04:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:04:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:04:46: 1000000 INFO @ Sun, 21 Jun 2020 17:04:51: 2000000 INFO @ Sun, 21 Jun 2020 17:04:52: #1 tag size is determined as 33 bps INFO @ Sun, 21 Jun 2020 17:04:52: #1 tag size = 33 INFO @ Sun, 21 Jun 2020 17:04:52: #1 total tags in treatment: 2115957 INFO @ Sun, 21 Jun 2020 17:04:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:04:52: #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 17:04:52: #1 tags after filtering in treatment: 2115925 INFO @ Sun, 21 Jun 2020 17:04:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:04:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:04:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:04:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:04:52: #2 number of paired peaks: 1126 INFO @ Sun, 21 Jun 2020 17:04:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:04:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:04:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:04:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:04:52: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 17:04:52: #2 alternative fragment length(s) may be 36,526,561 bps INFO @ Sun, 21 Jun 2020 17:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.05_model.r WARNING @ Sun, 21 Jun 2020 17:04:52: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:04:52: #2 You may need to consider one of the other alternative d(s): 36,526,561 WARNING @ Sun, 21 Jun 2020 17:04:52: #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 17:04:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:04:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.05_summits.bed INFO @ Sun, 21 Jun 2020 17:04:59: Done! pass1 - making usageList (380 chroms): 1 millis pass2 - checking and writing primary data (963 records, 4 fields): 11 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 @ Sun, 21 Jun 2020 17:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.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 17:05:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:05:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:05:16: 1000000 INFO @ Sun, 21 Jun 2020 17:05:22: 2000000 INFO @ Sun, 21 Jun 2020 17:05:22: #1 tag size is determined as 33 bps INFO @ Sun, 21 Jun 2020 17:05:22: #1 tag size = 33 INFO @ Sun, 21 Jun 2020 17:05:22: #1 total tags in treatment: 2115957 INFO @ Sun, 21 Jun 2020 17:05:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:05:22: #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 17:05:23: #1 tags after filtering in treatment: 2115925 INFO @ Sun, 21 Jun 2020 17:05:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:05:23: #1 finished! INFO @ Sun, 21 Jun 2020 17:05:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:05:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:05:23: #2 number of paired peaks: 1126 INFO @ Sun, 21 Jun 2020 17:05:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:05:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:05:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:05:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:05:23: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 17:05:23: #2 alternative fragment length(s) may be 36,526,561 bps INFO @ Sun, 21 Jun 2020 17:05:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.10_model.r WARNING @ Sun, 21 Jun 2020 17:05:23: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:05:23: #2 You may need to consider one of the other alternative d(s): 36,526,561 WARNING @ Sun, 21 Jun 2020 17:05:23: #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 17:05:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:05:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:05:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:05:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:05:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:05:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.10_summits.bed INFO @ Sun, 21 Jun 2020 17:05:30: Done! pass1 - making usageList (150 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 6 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 @ Sun, 21 Jun 2020 17:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.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 17:05:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:05:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:05:47: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:05:52: 2000000 INFO @ Sun, 21 Jun 2020 17:05:53: #1 tag size is determined as 33 bps INFO @ Sun, 21 Jun 2020 17:05:53: #1 tag size = 33 INFO @ Sun, 21 Jun 2020 17:05:53: #1 total tags in treatment: 2115957 INFO @ Sun, 21 Jun 2020 17:05:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:05:53: #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 17:05:53: #1 tags after filtering in treatment: 2115925 INFO @ Sun, 21 Jun 2020 17:05:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:05:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:05:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:05:53: #2 number of paired peaks: 1126 INFO @ Sun, 21 Jun 2020 17:05:53: start model_add_line... INFO @ Sun, 21 Jun 2020 17:05:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:05:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:05:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:05:54: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 17:05:54: #2 alternative fragment length(s) may be 36,526,561 bps INFO @ Sun, 21 Jun 2020 17:05:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.20_model.r WARNING @ Sun, 21 Jun 2020 17:05:54: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:05:54: #2 You may need to consider one of the other alternative d(s): 36,526,561 WARNING @ Sun, 21 Jun 2020 17:05:54: #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 17:05:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:05:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:05:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:06:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:06:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:06:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032417/SRX1032417.20_summits.bed INFO @ Sun, 21 Jun 2020 17:06:01: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (154 records, 4 fields): 4 millis CompletedMACS2peakCalling