Job ID = 5721130 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,465,535 reads read : 6,931,070 reads written : 6,931,070 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: 00:07:59 3465535 reads; of these: 3465535 (100.00%) were paired; of these: 696842 (20.11%) aligned concordantly 0 times 2062938 (59.53%) aligned concordantly exactly 1 time 705755 (20.36%) aligned concordantly >1 times ---- 696842 pairs aligned concordantly 0 times; of these: 358819 (51.49%) aligned discordantly 1 time ---- 338023 pairs aligned 0 times concordantly or discordantly; of these: 676046 mates make up the pairs; of these: 264269 (39.09%) aligned 0 times 175291 (25.93%) aligned exactly 1 time 236486 (34.98%) aligned >1 times 96.19% overall alignment rate Time searching: 00:07:59 Overall time: 00:07:59 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_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] 163755 / 3113568 = 0.0526 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 05:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.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 05:20:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:20:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:20:20: 1000000 INFO @ Thu, 16 Apr 2020 05:20:26: 2000000 INFO @ Thu, 16 Apr 2020 05:20:33: 3000000 INFO @ Thu, 16 Apr 2020 05:20:39: 4000000 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 05:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.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 05:20:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:20:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:20:45: 5000000 INFO @ Thu, 16 Apr 2020 05:20:51: 1000000 INFO @ Thu, 16 Apr 2020 05:20:52: 6000000 INFO @ Thu, 16 Apr 2020 05:20:54: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:20:54: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:20:54: #1 total tags in treatment: 2613040 INFO @ Thu, 16 Apr 2020 05:20:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:20:54: #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 05:20:54: #1 tags after filtering in treatment: 2525612 INFO @ Thu, 16 Apr 2020 05:20:54: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:20:54: #1 finished! INFO @ Thu, 16 Apr 2020 05:20:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:20:54: #2 number of paired peaks: 621 WARNING @ Thu, 16 Apr 2020 05:20:54: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Thu, 16 Apr 2020 05:20:54: start model_add_line... INFO @ Thu, 16 Apr 2020 05:20:54: start X-correlation... INFO @ Thu, 16 Apr 2020 05:20:54: end of X-cor INFO @ Thu, 16 Apr 2020 05:20:54: #2 finished! INFO @ Thu, 16 Apr 2020 05:20:54: #2 predicted fragment length is 135 bps INFO @ Thu, 16 Apr 2020 05:20:54: #2 alternative fragment length(s) may be 135 bps INFO @ Thu, 16 Apr 2020 05:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.05_model.r WARNING @ Thu, 16 Apr 2020 05:20:54: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:20:54: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Thu, 16 Apr 2020 05:20:54: #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 05:20:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:20:58: 2000000 INFO @ Thu, 16 Apr 2020 05:21:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:21:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:21:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:21:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.05_summits.bed INFO @ Thu, 16 Apr 2020 05:21:03: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (884 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:21:04: 3000000 INFO @ Thu, 16 Apr 2020 05:21:11: 4000000 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 05:21:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.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 05:21:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:21:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:21:17: 5000000 INFO @ Thu, 16 Apr 2020 05:21:22: 1000000 INFO @ Thu, 16 Apr 2020 05:21:24: 6000000 INFO @ Thu, 16 Apr 2020 05:21:27: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:21:27: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:21:27: #1 total tags in treatment: 2613040 INFO @ Thu, 16 Apr 2020 05:21:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:21:27: #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 05:21:27: #1 tags after filtering in treatment: 2525612 INFO @ Thu, 16 Apr 2020 05:21:27: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:21:27: #1 finished! INFO @ Thu, 16 Apr 2020 05:21:27: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:21:27: #2 number of paired peaks: 621 WARNING @ Thu, 16 Apr 2020 05:21:27: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Thu, 16 Apr 2020 05:21:27: start model_add_line... INFO @ Thu, 16 Apr 2020 05:21:27: start X-correlation... INFO @ Thu, 16 Apr 2020 05:21:27: end of X-cor INFO @ Thu, 16 Apr 2020 05:21:27: #2 finished! INFO @ Thu, 16 Apr 2020 05:21:27: #2 predicted fragment length is 135 bps INFO @ Thu, 16 Apr 2020 05:21:27: #2 alternative fragment length(s) may be 135 bps INFO @ Thu, 16 Apr 2020 05:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.10_model.r WARNING @ Thu, 16 Apr 2020 05:21:27: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:21:27: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Thu, 16 Apr 2020 05:21:27: #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 05:21:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:21:29: 2000000 INFO @ Thu, 16 Apr 2020 05:21:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:21:35: 3000000 INFO @ Thu, 16 Apr 2020 05:21:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:21:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:21:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.10_summits.bed INFO @ Thu, 16 Apr 2020 05:21:36: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (484 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:21:42: 4000000 INFO @ Thu, 16 Apr 2020 05:21:48: 5000000 INFO @ Thu, 16 Apr 2020 05:21:54: 6000000 INFO @ Thu, 16 Apr 2020 05:21:56: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:21:56: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:21:56: #1 total tags in treatment: 2613040 INFO @ Thu, 16 Apr 2020 05:21:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:21:56: #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 05:21:56: #1 tags after filtering in treatment: 2525612 INFO @ Thu, 16 Apr 2020 05:21:56: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:21:56: #1 finished! INFO @ Thu, 16 Apr 2020 05:21:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:21:57: #2 number of paired peaks: 621 WARNING @ Thu, 16 Apr 2020 05:21:57: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Thu, 16 Apr 2020 05:21:57: start model_add_line... INFO @ Thu, 16 Apr 2020 05:21:57: start X-correlation... INFO @ Thu, 16 Apr 2020 05:21:57: end of X-cor INFO @ Thu, 16 Apr 2020 05:21:57: #2 finished! INFO @ Thu, 16 Apr 2020 05:21:57: #2 predicted fragment length is 135 bps INFO @ Thu, 16 Apr 2020 05:21:57: #2 alternative fragment length(s) may be 135 bps INFO @ Thu, 16 Apr 2020 05:21:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.20_model.r WARNING @ Thu, 16 Apr 2020 05:21:57: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:21:57: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Thu, 16 Apr 2020 05:21:57: #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 05:21:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:22:02: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708272/SRX6708272.20_summits.bed INFO @ Thu, 16 Apr 2020 05:22:05: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (252 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。