Job ID = 5721070 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 17,924,449 reads read : 35,848,898 reads written : 35,848,898 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: 01:36:33 17924449 reads; of these: 17924449 (100.00%) were paired; of these: 5217908 (29.11%) aligned concordantly 0 times 6096832 (34.01%) aligned concordantly exactly 1 time 6609709 (36.88%) aligned concordantly >1 times ---- 5217908 pairs aligned concordantly 0 times; of these: 931592 (17.85%) aligned discordantly 1 time ---- 4286316 pairs aligned 0 times concordantly or discordantly; of these: 8572632 mates make up the pairs; of these: 4459535 (52.02%) aligned 0 times 2110126 (24.61%) aligned exactly 1 time 2002971 (23.36%) aligned >1 times 87.56% overall alignment rate Time searching: 01:36:33 Overall time: 01:36:33 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 24 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] 3634289 / 13213847 = 0.2750 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 06:21:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.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 06:21:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:21:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:21:24: 1000000 INFO @ Thu, 16 Apr 2020 06:21:32: 2000000 INFO @ Thu, 16 Apr 2020 06:21:39: 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 06:21:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.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 06:21:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:21:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:21:47: 4000000 INFO @ Thu, 16 Apr 2020 06:21:55: 5000000 INFO @ Thu, 16 Apr 2020 06:21:56: 1000000 INFO @ Thu, 16 Apr 2020 06:22:04: 6000000 INFO @ Thu, 16 Apr 2020 06:22:05: 2000000 INFO @ Thu, 16 Apr 2020 06:22:12: 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 06:22:15: 3000000 INFO @ Thu, 16 Apr 2020 06:22:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.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 06:22:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:22:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:22:21: 8000000 INFO @ Thu, 16 Apr 2020 06:22:24: 4000000 INFO @ Thu, 16 Apr 2020 06:22:25: 1000000 INFO @ Thu, 16 Apr 2020 06:22:30: 9000000 INFO @ Thu, 16 Apr 2020 06:22:33: 5000000 INFO @ Thu, 16 Apr 2020 06:22:34: 2000000 INFO @ Thu, 16 Apr 2020 06:22:38: 10000000 INFO @ Thu, 16 Apr 2020 06:22:42: 3000000 INFO @ Thu, 16 Apr 2020 06:22:43: 6000000 INFO @ Thu, 16 Apr 2020 06:22:47: 11000000 INFO @ Thu, 16 Apr 2020 06:22:51: 4000000 INFO @ Thu, 16 Apr 2020 06:22:52: 7000000 INFO @ Thu, 16 Apr 2020 06:22:55: 12000000 INFO @ Thu, 16 Apr 2020 06:23:00: 5000000 INFO @ Thu, 16 Apr 2020 06:23:02: 8000000 INFO @ Thu, 16 Apr 2020 06:23:04: 13000000 INFO @ Thu, 16 Apr 2020 06:23:08: 6000000 INFO @ Thu, 16 Apr 2020 06:23:11: 9000000 INFO @ Thu, 16 Apr 2020 06:23:13: 14000000 INFO @ Thu, 16 Apr 2020 06:23:17: 7000000 INFO @ Thu, 16 Apr 2020 06:23:21: 10000000 INFO @ Thu, 16 Apr 2020 06:23:21: 15000000 INFO @ Thu, 16 Apr 2020 06:23:26: 8000000 INFO @ Thu, 16 Apr 2020 06:23:30: 11000000 INFO @ Thu, 16 Apr 2020 06:23:30: 16000000 INFO @ Thu, 16 Apr 2020 06:23:34: 9000000 INFO @ Thu, 16 Apr 2020 06:23:39: 17000000 INFO @ Thu, 16 Apr 2020 06:23:40: 12000000 INFO @ Thu, 16 Apr 2020 06:23:43: 10000000 INFO @ Thu, 16 Apr 2020 06:23:47: 18000000 INFO @ Thu, 16 Apr 2020 06:23:49: 13000000 INFO @ Thu, 16 Apr 2020 06:23:52: 11000000 INFO @ Thu, 16 Apr 2020 06:23:56: 19000000 INFO @ Thu, 16 Apr 2020 06:23:59: 14000000 INFO @ Thu, 16 Apr 2020 06:24:00: 12000000 INFO @ Thu, 16 Apr 2020 06:24:04: 20000000 INFO @ Thu, 16 Apr 2020 06:24:08: 15000000 INFO @ Thu, 16 Apr 2020 06:24:09: 13000000 INFO @ Thu, 16 Apr 2020 06:24:13: 21000000 INFO @ Thu, 16 Apr 2020 06:24:18: 16000000 INFO @ Thu, 16 Apr 2020 06:24:18: 14000000 INFO @ Thu, 16 Apr 2020 06:24:22: 22000000 INFO @ Thu, 16 Apr 2020 06:24:27: 15000000 INFO @ Thu, 16 Apr 2020 06:24:27: 17000000 INFO @ Thu, 16 Apr 2020 06:24:30: 23000000 INFO @ Thu, 16 Apr 2020 06:24:36: 16000000 INFO @ Thu, 16 Apr 2020 06:24:37: 18000000 INFO @ Thu, 16 Apr 2020 06:24:39: 24000000 INFO @ Thu, 16 Apr 2020 06:24:40: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 06:24:40: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 06:24:40: #1 total tags in treatment: 9143188 INFO @ Thu, 16 Apr 2020 06:24:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:24:40: #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 06:24:40: #1 tags after filtering in treatment: 6557927 INFO @ Thu, 16 Apr 2020 06:24:40: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 16 Apr 2020 06:24:40: #1 finished! INFO @ Thu, 16 Apr 2020 06:24:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:24:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:24:41: #2 number of paired peaks: 7141 INFO @ Thu, 16 Apr 2020 06:24:41: start model_add_line... INFO @ Thu, 16 Apr 2020 06:24:41: start X-correlation... INFO @ Thu, 16 Apr 2020 06:24:41: end of X-cor INFO @ Thu, 16 Apr 2020 06:24:41: #2 finished! INFO @ Thu, 16 Apr 2020 06:24:41: #2 predicted fragment length is 225 bps INFO @ Thu, 16 Apr 2020 06:24:41: #2 alternative fragment length(s) may be 225 bps INFO @ Thu, 16 Apr 2020 06:24:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.05_model.r WARNING @ Thu, 16 Apr 2020 06:24:41: #2 Since the d (225) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:24:41: #2 You may need to consider one of the other alternative d(s): 225 WARNING @ Thu, 16 Apr 2020 06:24:41: #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 06:24:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:24:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:24:44: 17000000 INFO @ Thu, 16 Apr 2020 06:24:46: 19000000 INFO @ Thu, 16 Apr 2020 06:24:52: 18000000 INFO @ Thu, 16 Apr 2020 06:24:55: 20000000 INFO @ Thu, 16 Apr 2020 06:25:01: 19000000 INFO @ Thu, 16 Apr 2020 06:25:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:25:05: 21000000 INFO @ Thu, 16 Apr 2020 06:25:09: 20000000 INFO @ Thu, 16 Apr 2020 06:25:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:25:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:25:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.05_summits.bed INFO @ Thu, 16 Apr 2020 06:25:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (13885 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:25:14: 22000000 INFO @ Thu, 16 Apr 2020 06:25:17: 21000000 INFO @ Thu, 16 Apr 2020 06:25:24: 23000000 INFO @ Thu, 16 Apr 2020 06:25:26: 22000000 INFO @ Thu, 16 Apr 2020 06:25:33: 24000000 INFO @ Thu, 16 Apr 2020 06:25:34: 23000000 INFO @ Thu, 16 Apr 2020 06:25:34: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 06:25:34: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 06:25:34: #1 total tags in treatment: 9143188 INFO @ Thu, 16 Apr 2020 06:25:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:25:34: #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 06:25:34: #1 tags after filtering in treatment: 6557927 INFO @ Thu, 16 Apr 2020 06:25:34: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 16 Apr 2020 06:25:34: #1 finished! INFO @ Thu, 16 Apr 2020 06:25:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:25:35: #2 number of paired peaks: 7141 INFO @ Thu, 16 Apr 2020 06:25:35: start model_add_line... INFO @ Thu, 16 Apr 2020 06:25:35: start X-correlation... INFO @ Thu, 16 Apr 2020 06:25:35: end of X-cor INFO @ Thu, 16 Apr 2020 06:25:35: #2 finished! INFO @ Thu, 16 Apr 2020 06:25:35: #2 predicted fragment length is 225 bps INFO @ Thu, 16 Apr 2020 06:25:35: #2 alternative fragment length(s) may be 225 bps INFO @ Thu, 16 Apr 2020 06:25:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.10_model.r WARNING @ Thu, 16 Apr 2020 06:25:35: #2 Since the d (225) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:25:35: #2 You may need to consider one of the other alternative d(s): 225 WARNING @ Thu, 16 Apr 2020 06:25:35: #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 06:25:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:25:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:25:42: 24000000 INFO @ Thu, 16 Apr 2020 06:25:43: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 06:25:43: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 06:25:43: #1 total tags in treatment: 9143188 INFO @ Thu, 16 Apr 2020 06:25:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:25:43: #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 06:25:43: #1 tags after filtering in treatment: 6557927 INFO @ Thu, 16 Apr 2020 06:25:43: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 16 Apr 2020 06:25:43: #1 finished! INFO @ Thu, 16 Apr 2020 06:25:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:25:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:25:44: #2 number of paired peaks: 7141 INFO @ Thu, 16 Apr 2020 06:25:44: start model_add_line... INFO @ Thu, 16 Apr 2020 06:25:44: start X-correlation... INFO @ Thu, 16 Apr 2020 06:25:44: end of X-cor INFO @ Thu, 16 Apr 2020 06:25:44: #2 finished! INFO @ Thu, 16 Apr 2020 06:25:44: #2 predicted fragment length is 225 bps INFO @ Thu, 16 Apr 2020 06:25:44: #2 alternative fragment length(s) may be 225 bps INFO @ Thu, 16 Apr 2020 06:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.20_model.r WARNING @ Thu, 16 Apr 2020 06:25:44: #2 Since the d (225) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:25:44: #2 You may need to consider one of the other alternative d(s): 225 WARNING @ Thu, 16 Apr 2020 06:25:44: #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 06:25:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:25:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 06:25:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:26:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.10_summits.bed INFO @ Thu, 16 Apr 2020 06:26:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (10258 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:26:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:26:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:26:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448068/SRX6448068.20_summits.bed INFO @ Thu, 16 Apr 2020 06:26:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6276 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。