Job ID = 5721065 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,787,373 reads read : 9,574,746 reads written : 9,574,746 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: 00:19:33 4787373 reads; of these: 4787373 (100.00%) were paired; of these: 592965 (12.39%) aligned concordantly 0 times 2909203 (60.77%) aligned concordantly exactly 1 time 1285205 (26.85%) aligned concordantly >1 times ---- 592965 pairs aligned concordantly 0 times; of these: 294059 (49.59%) aligned discordantly 1 time ---- 298906 pairs aligned 0 times concordantly or discordantly; of these: 597812 mates make up the pairs; of these: 218350 (36.52%) aligned 0 times 101201 (16.93%) aligned exactly 1 time 278261 (46.55%) aligned >1 times 97.72% overall alignment rate Time searching: 00:19:33 Overall time: 00:19:33 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] 530195 / 4428208 = 0.1197 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 04:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.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 04:28:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:28:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:28:39: 1000000 INFO @ Thu, 16 Apr 2020 04:28:46: 2000000 INFO @ Thu, 16 Apr 2020 04:28:54: 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 04:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.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 04:29:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:29:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:29:02: 4000000 INFO @ Thu, 16 Apr 2020 04:29:09: 1000000 INFO @ Thu, 16 Apr 2020 04:29:10: 5000000 INFO @ Thu, 16 Apr 2020 04:29:16: 2000000 INFO @ Thu, 16 Apr 2020 04:29:18: 6000000 INFO @ Thu, 16 Apr 2020 04:29:24: 3000000 INFO @ Thu, 16 Apr 2020 04:29:26: 7000000 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 04:29:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.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 04:29:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:29:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:29:32: 4000000 INFO @ Thu, 16 Apr 2020 04:29:34: 8000000 INFO @ Thu, 16 Apr 2020 04:29:36: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:29:36: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:29:36: #1 total tags in treatment: 3684278 INFO @ Thu, 16 Apr 2020 04:29:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:29:36: #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 04:29:36: #1 tags after filtering in treatment: 3539601 INFO @ Thu, 16 Apr 2020 04:29:36: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 04:29:36: #1 finished! INFO @ Thu, 16 Apr 2020 04:29:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:29:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:29:37: #2 number of paired peaks: 1114 INFO @ Thu, 16 Apr 2020 04:29:37: start model_add_line... INFO @ Thu, 16 Apr 2020 04:29:37: start X-correlation... INFO @ Thu, 16 Apr 2020 04:29:37: end of X-cor INFO @ Thu, 16 Apr 2020 04:29:37: #2 finished! INFO @ Thu, 16 Apr 2020 04:29:37: #2 predicted fragment length is 199 bps INFO @ Thu, 16 Apr 2020 04:29:37: #2 alternative fragment length(s) may be 199 bps INFO @ Thu, 16 Apr 2020 04:29:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.05_model.r WARNING @ Thu, 16 Apr 2020 04:29:37: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:29:37: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Thu, 16 Apr 2020 04:29:37: #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 04:29:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:29:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:29:39: 1000000 INFO @ Thu, 16 Apr 2020 04:29:40: 5000000 INFO @ Thu, 16 Apr 2020 04:29:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:29:47: 2000000 INFO @ Thu, 16 Apr 2020 04:29:48: 6000000 INFO @ Thu, 16 Apr 2020 04:29:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:29:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:29:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.05_summits.bed INFO @ Thu, 16 Apr 2020 04:29:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1359 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:29:55: 3000000 INFO @ Thu, 16 Apr 2020 04:29:56: 7000000 INFO @ Thu, 16 Apr 2020 04:30:02: 4000000 INFO @ Thu, 16 Apr 2020 04:30:04: 8000000 INFO @ Thu, 16 Apr 2020 04:30:06: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:30:06: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:30:06: #1 total tags in treatment: 3684278 INFO @ Thu, 16 Apr 2020 04:30:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:30:06: #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 04:30:06: #1 tags after filtering in treatment: 3539601 INFO @ Thu, 16 Apr 2020 04:30:06: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 04:30:06: #1 finished! INFO @ Thu, 16 Apr 2020 04:30:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:30:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:30:07: #2 number of paired peaks: 1114 INFO @ Thu, 16 Apr 2020 04:30:07: start model_add_line... INFO @ Thu, 16 Apr 2020 04:30:07: start X-correlation... INFO @ Thu, 16 Apr 2020 04:30:07: end of X-cor INFO @ Thu, 16 Apr 2020 04:30:07: #2 finished! INFO @ Thu, 16 Apr 2020 04:30:07: #2 predicted fragment length is 199 bps INFO @ Thu, 16 Apr 2020 04:30:07: #2 alternative fragment length(s) may be 199 bps INFO @ Thu, 16 Apr 2020 04:30:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.10_model.r WARNING @ Thu, 16 Apr 2020 04:30:07: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:30:07: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Thu, 16 Apr 2020 04:30:07: #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 04:30:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:30:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:30:10: 5000000 INFO @ Thu, 16 Apr 2020 04:30:15: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:30:18: 6000000 INFO @ Thu, 16 Apr 2020 04:30:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:30:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:30:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.10_summits.bed INFO @ Thu, 16 Apr 2020 04:30:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (756 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:30:26: 7000000 INFO @ Thu, 16 Apr 2020 04:30:34: 8000000 INFO @ Thu, 16 Apr 2020 04:30:36: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:30:36: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:30:36: #1 total tags in treatment: 3684278 INFO @ Thu, 16 Apr 2020 04:30:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:30:36: #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 04:30:36: #1 tags after filtering in treatment: 3539601 INFO @ Thu, 16 Apr 2020 04:30:36: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 04:30:36: #1 finished! INFO @ Thu, 16 Apr 2020 04:30:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:30:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:30:37: #2 number of paired peaks: 1114 INFO @ Thu, 16 Apr 2020 04:30:37: start model_add_line... INFO @ Thu, 16 Apr 2020 04:30:37: start X-correlation... INFO @ Thu, 16 Apr 2020 04:30:37: end of X-cor INFO @ Thu, 16 Apr 2020 04:30:37: #2 finished! INFO @ Thu, 16 Apr 2020 04:30:37: #2 predicted fragment length is 199 bps INFO @ Thu, 16 Apr 2020 04:30:37: #2 alternative fragment length(s) may be 199 bps INFO @ Thu, 16 Apr 2020 04:30:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.20_model.r WARNING @ Thu, 16 Apr 2020 04:30:37: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:30:37: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Thu, 16 Apr 2020 04:30:37: #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 04:30:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:30:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:30:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:30:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:30:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:30:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448063/SRX6448063.20_summits.bed INFO @ Thu, 16 Apr 2020 04:30:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (391 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。