Job ID = 5721060 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,057,274 reads read : 8,114,548 reads written : 8,114,548 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:15:05 4057274 reads; of these: 4057274 (100.00%) were paired; of these: 514614 (12.68%) aligned concordantly 0 times 2513796 (61.96%) aligned concordantly exactly 1 time 1028864 (25.36%) aligned concordantly >1 times ---- 514614 pairs aligned concordantly 0 times; of these: 265124 (51.52%) aligned discordantly 1 time ---- 249490 pairs aligned 0 times concordantly or discordantly; of these: 498980 mates make up the pairs; of these: 182744 (36.62%) aligned 0 times 83239 (16.68%) aligned exactly 1 time 232997 (46.69%) aligned >1 times 97.75% overall alignment rate Time searching: 00:15:05 Overall time: 00:15:05 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_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 415964 / 3755890 = 0.1107 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 @ Thu, 16 Apr 2020 04:17:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.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 @ Thu, 16 Apr 2020 04:17:37: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:17:37: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:17:44: 1000000 INFO @ Thu, 16 Apr 2020 04:17:52: 2000000 INFO @ Thu, 16 Apr 2020 04:17:59: 3000000 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 @ Thu, 16 Apr 2020 04:18:06: 4000000 INFO @ Thu, 16 Apr 2020 04:18:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.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 @ Thu, 16 Apr 2020 04:18:07: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:18:07: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:18:14: 5000000 INFO @ Thu, 16 Apr 2020 04:18:16: 1000000 INFO @ Thu, 16 Apr 2020 04:18:24: 6000000 INFO @ Thu, 16 Apr 2020 04:18:25: 2000000 INFO @ Thu, 16 Apr 2020 04:18:33: 7000000 INFO @ Thu, 16 Apr 2020 04:18:34: 3000000 INFO @ Thu, 16 Apr 2020 04:18:34: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:18:34: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:18:34: #1 total tags in treatment: 3144437 INFO @ Thu, 16 Apr 2020 04:18:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:18:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:18:34: #1 tags after filtering in treatment: 3037764 INFO @ Thu, 16 Apr 2020 04:18:34: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:18:34: #1 finished! INFO @ Thu, 16 Apr 2020 04:18:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:18:34: #2 number of paired peaks: 1230 INFO @ Thu, 16 Apr 2020 04:18:34: start model_add_line... INFO @ Thu, 16 Apr 2020 04:18:34: start X-correlation... INFO @ Thu, 16 Apr 2020 04:18:34: end of X-cor INFO @ Thu, 16 Apr 2020 04:18:34: #2 finished! INFO @ Thu, 16 Apr 2020 04:18:34: #2 predicted fragment length is 192 bps INFO @ Thu, 16 Apr 2020 04:18:34: #2 alternative fragment length(s) may be 192 bps INFO @ Thu, 16 Apr 2020 04:18:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.05_model.r WARNING @ Thu, 16 Apr 2020 04:18:34: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:18:34: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Thu, 16 Apr 2020 04:18:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 04:18:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:18:34: #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 @ Thu, 16 Apr 2020 04:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.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 @ Thu, 16 Apr 2020 04:18:37: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:18:37: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:18:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:18:43: 4000000 INFO @ Thu, 16 Apr 2020 04:18:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:18:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:18:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.05_summits.bed INFO @ Thu, 16 Apr 2020 04:18:44: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1259 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:18:47: 1000000 INFO @ Thu, 16 Apr 2020 04:18:52: 5000000 INFO @ Thu, 16 Apr 2020 04:18:56: 2000000 INFO @ Thu, 16 Apr 2020 04:19:01: 6000000 INFO @ Thu, 16 Apr 2020 04:19:05: 3000000 INFO @ Thu, 16 Apr 2020 04:19:10: 7000000 INFO @ Thu, 16 Apr 2020 04:19:10: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:19:10: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:19:10: #1 total tags in treatment: 3144437 INFO @ Thu, 16 Apr 2020 04:19:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:19:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:19:10: #1 tags after filtering in treatment: 3037764 INFO @ Thu, 16 Apr 2020 04:19:10: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:19:10: #1 finished! INFO @ Thu, 16 Apr 2020 04:19:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:19:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:19:11: #2 number of paired peaks: 1230 INFO @ Thu, 16 Apr 2020 04:19:11: start model_add_line... INFO @ Thu, 16 Apr 2020 04:19:11: start X-correlation... INFO @ Thu, 16 Apr 2020 04:19:11: end of X-cor INFO @ Thu, 16 Apr 2020 04:19:11: #2 finished! INFO @ Thu, 16 Apr 2020 04:19:11: #2 predicted fragment length is 192 bps INFO @ Thu, 16 Apr 2020 04:19:11: #2 alternative fragment length(s) may be 192 bps INFO @ Thu, 16 Apr 2020 04:19:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.10_model.r WARNING @ Thu, 16 Apr 2020 04:19:11: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:19:11: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Thu, 16 Apr 2020 04:19:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 04:19:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:19:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:19:14: 4000000 INFO @ Thu, 16 Apr 2020 04:19:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:19:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:19:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:19:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.10_summits.bed INFO @ Thu, 16 Apr 2020 04:19:21: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (721 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:19:22: 5000000 INFO @ Thu, 16 Apr 2020 04:19:30: 6000000 INFO @ Thu, 16 Apr 2020 04:19:38: 7000000 INFO @ Thu, 16 Apr 2020 04:19:39: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:19:39: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:19:39: #1 total tags in treatment: 3144437 INFO @ Thu, 16 Apr 2020 04:19:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:19:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:19:39: #1 tags after filtering in treatment: 3037764 INFO @ Thu, 16 Apr 2020 04:19:39: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:19:39: #1 finished! INFO @ Thu, 16 Apr 2020 04:19:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:19:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:19:40: #2 number of paired peaks: 1230 INFO @ Thu, 16 Apr 2020 04:19:40: start model_add_line... INFO @ Thu, 16 Apr 2020 04:19:40: start X-correlation... INFO @ Thu, 16 Apr 2020 04:19:40: end of X-cor INFO @ Thu, 16 Apr 2020 04:19:40: #2 finished! INFO @ Thu, 16 Apr 2020 04:19:40: #2 predicted fragment length is 192 bps INFO @ Thu, 16 Apr 2020 04:19:40: #2 alternative fragment length(s) may be 192 bps INFO @ Thu, 16 Apr 2020 04:19:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.20_model.r WARNING @ Thu, 16 Apr 2020 04:19:40: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:19:40: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Thu, 16 Apr 2020 04:19:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 04:19:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:19:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:19:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:19:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:19:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:19:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448058/SRX6448058.20_summits.bed INFO @ Thu, 16 Apr 2020 04:19:50: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (345 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。