Job ID = 5721075 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,143,177 reads read : 16,286,354 reads written : 16,286,354 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: 00:45:40 8143177 reads; of these: 8143177 (100.00%) were paired; of these: 2253111 (27.67%) aligned concordantly 0 times 2872460 (35.27%) aligned concordantly exactly 1 time 3017606 (37.06%) aligned concordantly >1 times ---- 2253111 pairs aligned concordantly 0 times; of these: 424579 (18.84%) aligned discordantly 1 time ---- 1828532 pairs aligned 0 times concordantly or discordantly; of these: 3657064 mates make up the pairs; of these: 1905031 (52.09%) aligned 0 times 962944 (26.33%) aligned exactly 1 time 789089 (21.58%) aligned >1 times 88.30% overall alignment rate Time searching: 00:45:40 Overall time: 00:45:40 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 12 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] 1446836 / 6119347 = 0.2364 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 05:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.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 05:08:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:08: 1000000 INFO @ Thu, 16 Apr 2020 05:08:15: 2000000 INFO @ Thu, 16 Apr 2020 05:08:23: 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 05:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.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 05:08:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:31: 4000000 INFO @ Thu, 16 Apr 2020 05:08:40: 1000000 INFO @ Thu, 16 Apr 2020 05:08:41: 5000000 INFO @ Thu, 16 Apr 2020 05:08:50: 2000000 INFO @ Thu, 16 Apr 2020 05:08:50: 6000000 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 05:08:59: 3000000 INFO @ Thu, 16 Apr 2020 05:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.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 05:09:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:09:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:09:00: 7000000 INFO @ Thu, 16 Apr 2020 05:09:08: 4000000 INFO @ Thu, 16 Apr 2020 05:09:10: 1000000 INFO @ Thu, 16 Apr 2020 05:09:10: 8000000 INFO @ Thu, 16 Apr 2020 05:09:18: 5000000 INFO @ Thu, 16 Apr 2020 05:09:20: 2000000 INFO @ Thu, 16 Apr 2020 05:09:20: 9000000 INFO @ Thu, 16 Apr 2020 05:09:27: 6000000 INFO @ Thu, 16 Apr 2020 05:09:29: 3000000 INFO @ Thu, 16 Apr 2020 05:09:30: 10000000 INFO @ Thu, 16 Apr 2020 05:09:37: 7000000 INFO @ Thu, 16 Apr 2020 05:09:39: 4000000 INFO @ Thu, 16 Apr 2020 05:09:40: 11000000 INFO @ Thu, 16 Apr 2020 05:09:44: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:09:44: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:09:44: #1 total tags in treatment: 4465568 INFO @ Thu, 16 Apr 2020 05:09:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:09:44: #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 05:09:44: #1 tags after filtering in treatment: 3485277 INFO @ Thu, 16 Apr 2020 05:09:44: #1 Redundant rate of treatment: 0.22 INFO @ Thu, 16 Apr 2020 05:09:44: #1 finished! INFO @ Thu, 16 Apr 2020 05:09:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:09:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:09:45: #2 number of paired peaks: 6335 INFO @ Thu, 16 Apr 2020 05:09:45: start model_add_line... INFO @ Thu, 16 Apr 2020 05:09:45: start X-correlation... INFO @ Thu, 16 Apr 2020 05:09:45: end of X-cor INFO @ Thu, 16 Apr 2020 05:09:45: #2 finished! INFO @ Thu, 16 Apr 2020 05:09:45: #2 predicted fragment length is 222 bps INFO @ Thu, 16 Apr 2020 05:09:45: #2 alternative fragment length(s) may be 222 bps INFO @ Thu, 16 Apr 2020 05:09:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.05_model.r WARNING @ Thu, 16 Apr 2020 05:09:45: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:09:45: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Thu, 16 Apr 2020 05:09:45: #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 05:09:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:09:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:09:46: 8000000 INFO @ Thu, 16 Apr 2020 05:09:48: 5000000 INFO @ Thu, 16 Apr 2020 05:09:56: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:09:56: 9000000 INFO @ Thu, 16 Apr 2020 05:09:58: 6000000 INFO @ Thu, 16 Apr 2020 05:10:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:10:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:10:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.05_summits.bed INFO @ Thu, 16 Apr 2020 05:10:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9826 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:10:06: 10000000 INFO @ Thu, 16 Apr 2020 05:10:07: 7000000 INFO @ Thu, 16 Apr 2020 05:10:15: 11000000 INFO @ Thu, 16 Apr 2020 05:10:17: 8000000 INFO @ Thu, 16 Apr 2020 05:10:20: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:10:20: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:10:20: #1 total tags in treatment: 4465568 INFO @ Thu, 16 Apr 2020 05:10:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:10:20: #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 05:10:20: #1 tags after filtering in treatment: 3485277 INFO @ Thu, 16 Apr 2020 05:10:20: #1 Redundant rate of treatment: 0.22 INFO @ Thu, 16 Apr 2020 05:10:20: #1 finished! INFO @ Thu, 16 Apr 2020 05:10:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:10:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:10:20: #2 number of paired peaks: 6335 INFO @ Thu, 16 Apr 2020 05:10:20: start model_add_line... INFO @ Thu, 16 Apr 2020 05:10:20: start X-correlation... INFO @ Thu, 16 Apr 2020 05:10:20: end of X-cor INFO @ Thu, 16 Apr 2020 05:10:20: #2 finished! INFO @ Thu, 16 Apr 2020 05:10:20: #2 predicted fragment length is 222 bps INFO @ Thu, 16 Apr 2020 05:10:20: #2 alternative fragment length(s) may be 222 bps INFO @ Thu, 16 Apr 2020 05:10:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.10_model.r WARNING @ Thu, 16 Apr 2020 05:10:20: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:10:20: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Thu, 16 Apr 2020 05:10:20: #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 05:10:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:10:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:10:26: 9000000 INFO @ Thu, 16 Apr 2020 05:10:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:10:34: 10000000 INFO @ Thu, 16 Apr 2020 05:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.10_summits.bed INFO @ Thu, 16 Apr 2020 05:10:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6267 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:10:43: 11000000 INFO @ Thu, 16 Apr 2020 05:10:47: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:10:47: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:10:47: #1 total tags in treatment: 4465568 INFO @ Thu, 16 Apr 2020 05:10:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:10:47: #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 05:10:47: #1 tags after filtering in treatment: 3485277 INFO @ Thu, 16 Apr 2020 05:10:47: #1 Redundant rate of treatment: 0.22 INFO @ Thu, 16 Apr 2020 05:10:47: #1 finished! INFO @ Thu, 16 Apr 2020 05:10:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:10:47: #2 number of paired peaks: 6335 INFO @ Thu, 16 Apr 2020 05:10:47: start model_add_line... INFO @ Thu, 16 Apr 2020 05:10:47: start X-correlation... INFO @ Thu, 16 Apr 2020 05:10:47: end of X-cor INFO @ Thu, 16 Apr 2020 05:10:47: #2 finished! INFO @ Thu, 16 Apr 2020 05:10:47: #2 predicted fragment length is 222 bps INFO @ Thu, 16 Apr 2020 05:10:47: #2 alternative fragment length(s) may be 222 bps INFO @ Thu, 16 Apr 2020 05:10:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.20_model.r WARNING @ Thu, 16 Apr 2020 05:10:47: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:10:47: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Thu, 16 Apr 2020 05:10:47: #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 05:10:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:10:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 05:11:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:11:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:11:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448071/SRX6448071.20_summits.bed INFO @ Thu, 16 Apr 2020 05:11:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3510 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。