Job ID = 5721047 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,554,576 reads read : 25,109,152 reads written : 25,109,152 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: 00:35:58 12554576 reads; of these: 12554576 (100.00%) were paired; of these: 8822701 (70.27%) aligned concordantly 0 times 1191432 (9.49%) aligned concordantly exactly 1 time 2540443 (20.24%) aligned concordantly >1 times ---- 8822701 pairs aligned concordantly 0 times; of these: 137145 (1.55%) aligned discordantly 1 time ---- 8685556 pairs aligned 0 times concordantly or discordantly; of these: 17371112 mates make up the pairs; of these: 16525916 (95.13%) aligned 0 times 203927 (1.17%) aligned exactly 1 time 641269 (3.69%) aligned >1 times 34.18% overall alignment rate Time searching: 00:35:58 Overall time: 00:35:58 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] 2647668 / 3816299 = 0.6938 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 04:48:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.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 04:48:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:48:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:49:01: 1000000 INFO @ Thu, 16 Apr 2020 04:49:11: 2000000 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 04:49:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.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 04:49:20: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:49:20: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:49:21: 3000000 INFO @ Thu, 16 Apr 2020 04:49:25: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 04:49:25: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 04:49:25: #1 total tags in treatment: 1177689 INFO @ Thu, 16 Apr 2020 04:49:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:49:25: #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 04:49:25: #1 tags after filtering in treatment: 847815 INFO @ Thu, 16 Apr 2020 04:49:25: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 16 Apr 2020 04:49:25: #1 finished! INFO @ Thu, 16 Apr 2020 04:49:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:49:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:49:25: #2 number of paired peaks: 6153 INFO @ Thu, 16 Apr 2020 04:49:25: start model_add_line... INFO @ Thu, 16 Apr 2020 04:49:25: start X-correlation... INFO @ Thu, 16 Apr 2020 04:49:25: end of X-cor INFO @ Thu, 16 Apr 2020 04:49:25: #2 finished! INFO @ Thu, 16 Apr 2020 04:49:25: #2 predicted fragment length is 264 bps INFO @ Thu, 16 Apr 2020 04:49:25: #2 alternative fragment length(s) may be 264 bps INFO @ Thu, 16 Apr 2020 04:49:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.05_model.r WARNING @ Thu, 16 Apr 2020 04:49:25: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:49:25: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Thu, 16 Apr 2020 04:49:25: #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 04:49:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:49:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.05_summits.bed INFO @ Thu, 16 Apr 2020 04:49:28: Done! INFO @ Thu, 16 Apr 2020 04:49:30: 1000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4462 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:49:41: 2000000 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 04:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.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 04:49:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:49:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:49:51: 3000000 INFO @ Thu, 16 Apr 2020 04:49:54: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 04:49:54: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 04:49:54: #1 total tags in treatment: 1177689 INFO @ Thu, 16 Apr 2020 04:49:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:49:54: #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 04:49:54: #1 tags after filtering in treatment: 847815 INFO @ Thu, 16 Apr 2020 04:49:54: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 16 Apr 2020 04:49:54: #1 finished! INFO @ Thu, 16 Apr 2020 04:49:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:49:54: #2 number of paired peaks: 6153 INFO @ Thu, 16 Apr 2020 04:49:54: start model_add_line... INFO @ Thu, 16 Apr 2020 04:49:54: start X-correlation... INFO @ Thu, 16 Apr 2020 04:49:54: end of X-cor INFO @ Thu, 16 Apr 2020 04:49:54: #2 finished! INFO @ Thu, 16 Apr 2020 04:49:54: #2 predicted fragment length is 264 bps INFO @ Thu, 16 Apr 2020 04:49:54: #2 alternative fragment length(s) may be 264 bps INFO @ Thu, 16 Apr 2020 04:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.10_model.r WARNING @ Thu, 16 Apr 2020 04:49:54: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:49:54: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Thu, 16 Apr 2020 04:49:54: #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 04:49:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:49:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:49:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:49:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:49:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.10_summits.bed INFO @ Thu, 16 Apr 2020 04:49:58: Done! INFO @ Thu, 16 Apr 2020 04:50:01: 1000000 pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2852 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:50:12: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 04:50:22: 3000000 BigWig に変換しました。 INFO @ Thu, 16 Apr 2020 04:50:25: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 04:50:25: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 04:50:25: #1 total tags in treatment: 1177689 INFO @ Thu, 16 Apr 2020 04:50:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:50:25: #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 04:50:25: #1 tags after filtering in treatment: 847815 INFO @ Thu, 16 Apr 2020 04:50:25: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 16 Apr 2020 04:50:25: #1 finished! INFO @ Thu, 16 Apr 2020 04:50:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:50:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:50:25: #2 number of paired peaks: 6153 INFO @ Thu, 16 Apr 2020 04:50:25: start model_add_line... INFO @ Thu, 16 Apr 2020 04:50:25: start X-correlation... INFO @ Thu, 16 Apr 2020 04:50:25: end of X-cor INFO @ Thu, 16 Apr 2020 04:50:25: #2 finished! INFO @ Thu, 16 Apr 2020 04:50:25: #2 predicted fragment length is 264 bps INFO @ Thu, 16 Apr 2020 04:50:25: #2 alternative fragment length(s) may be 264 bps INFO @ Thu, 16 Apr 2020 04:50:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.20_model.r WARNING @ Thu, 16 Apr 2020 04:50:25: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:50:25: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Thu, 16 Apr 2020 04:50:25: #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 04:50:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:50:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:50:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:50:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:50:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:50:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386780/SRX6386780.20_summits.bed INFO @ Thu, 16 Apr 2020 04:50:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1480 records, 4 fields): 2 millis CompletedMACS2peakCalling