Job ID = 5721069 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,270,767 reads read : 6,541,534 reads written : 6,541,534 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:31 3270767 reads; of these: 3270767 (100.00%) were paired; of these: 495909 (15.16%) aligned concordantly 0 times 1948609 (59.58%) aligned concordantly exactly 1 time 826249 (25.26%) aligned concordantly >1 times ---- 495909 pairs aligned concordantly 0 times; of these: 268385 (54.12%) aligned discordantly 1 time ---- 227524 pairs aligned 0 times concordantly or discordantly; of these: 455048 mates make up the pairs; of these: 148539 (32.64%) aligned 0 times 80848 (17.77%) aligned exactly 1 time 225661 (49.59%) aligned >1 times 97.73% overall alignment rate Time searching: 00:12:32 Overall time: 00:12:32 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] 347255 / 3002633 = 0.1157 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 04:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.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 04:19:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:19:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:19:13: 1000000 INFO @ Thu, 16 Apr 2020 04:19:21: 2000000 INFO @ Thu, 16 Apr 2020 04:19:28: 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 04:19:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.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 04:19:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:19:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:19:36: 4000000 INFO @ Thu, 16 Apr 2020 04:19:45: 1000000 INFO @ Thu, 16 Apr 2020 04:19:46: 5000000 INFO @ Thu, 16 Apr 2020 04:19:53: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:19:53: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:19:53: #1 total tags in treatment: 2445818 INFO @ Thu, 16 Apr 2020 04:19:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:19:53: #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 04:19:53: #1 tags after filtering in treatment: 2371333 INFO @ Thu, 16 Apr 2020 04:19:53: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:19:53: #1 finished! INFO @ Thu, 16 Apr 2020 04:19:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:19:53: #2 number of paired peaks: 1208 INFO @ Thu, 16 Apr 2020 04:19:53: start model_add_line... INFO @ Thu, 16 Apr 2020 04:19:53: start X-correlation... INFO @ Thu, 16 Apr 2020 04:19:53: end of X-cor INFO @ Thu, 16 Apr 2020 04:19:53: #2 finished! INFO @ Thu, 16 Apr 2020 04:19:53: #2 predicted fragment length is 203 bps INFO @ Thu, 16 Apr 2020 04:19:53: #2 alternative fragment length(s) may be 203 bps INFO @ Thu, 16 Apr 2020 04:19:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.05_model.r WARNING @ Thu, 16 Apr 2020 04:19:53: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:19:53: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Thu, 16 Apr 2020 04:19:53: #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 04:19:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:19:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:19:56: 2000000 INFO @ Thu, 16 Apr 2020 04:19:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:20:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:20:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:20:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.05_summits.bed INFO @ Thu, 16 Apr 2020 04:20:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (985 records, 4 fields): 3 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 @ Thu, 16 Apr 2020 04:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.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 04:20:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:20:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:20:06: 3000000 INFO @ Thu, 16 Apr 2020 04:20:15: 1000000 INFO @ Thu, 16 Apr 2020 04:20:17: 4000000 INFO @ Thu, 16 Apr 2020 04:20:25: 2000000 INFO @ Thu, 16 Apr 2020 04:20:28: 5000000 INFO @ Thu, 16 Apr 2020 04:20:34: 3000000 INFO @ Thu, 16 Apr 2020 04:20:36: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:20:36: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:20:36: #1 total tags in treatment: 2445818 INFO @ Thu, 16 Apr 2020 04:20:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:20:36: #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 04:20:36: #1 tags after filtering in treatment: 2371333 INFO @ Thu, 16 Apr 2020 04:20:36: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:20:36: #1 finished! INFO @ Thu, 16 Apr 2020 04:20:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:20:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:20:36: #2 number of paired peaks: 1208 INFO @ Thu, 16 Apr 2020 04:20:36: start model_add_line... INFO @ Thu, 16 Apr 2020 04:20:37: start X-correlation... INFO @ Thu, 16 Apr 2020 04:20:37: end of X-cor INFO @ Thu, 16 Apr 2020 04:20:37: #2 finished! INFO @ Thu, 16 Apr 2020 04:20:37: #2 predicted fragment length is 203 bps INFO @ Thu, 16 Apr 2020 04:20:37: #2 alternative fragment length(s) may be 203 bps INFO @ Thu, 16 Apr 2020 04:20:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.10_model.r WARNING @ Thu, 16 Apr 2020 04:20:37: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:20:37: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Thu, 16 Apr 2020 04:20:37: #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 04:20:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:20:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:20:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:20:43: 4000000 INFO @ Thu, 16 Apr 2020 04:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.10_summits.bed INFO @ Thu, 16 Apr 2020 04:20:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (550 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:20:52: 5000000 INFO @ Thu, 16 Apr 2020 04:20:58: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:20:58: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:20:58: #1 total tags in treatment: 2445818 INFO @ Thu, 16 Apr 2020 04:20:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:20:58: #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 04:20:58: #1 tags after filtering in treatment: 2371333 INFO @ Thu, 16 Apr 2020 04:20:58: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:20:58: #1 finished! INFO @ Thu, 16 Apr 2020 04:20:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:20:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:20:58: #2 number of paired peaks: 1208 INFO @ Thu, 16 Apr 2020 04:20:58: start model_add_line... INFO @ Thu, 16 Apr 2020 04:20:58: start X-correlation... INFO @ Thu, 16 Apr 2020 04:20:58: end of X-cor INFO @ Thu, 16 Apr 2020 04:20:58: #2 finished! INFO @ Thu, 16 Apr 2020 04:20:58: #2 predicted fragment length is 203 bps INFO @ Thu, 16 Apr 2020 04:20:58: #2 alternative fragment length(s) may be 203 bps INFO @ Thu, 16 Apr 2020 04:20:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.20_model.r WARNING @ Thu, 16 Apr 2020 04:20:58: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:20:58: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Thu, 16 Apr 2020 04:20:58: #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 04:20:58: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:20:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:21:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:21:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:21:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:21:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448067/SRX6448067.20_summits.bed INFO @ Thu, 16 Apr 2020 04:21:06: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (279 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。