Job ID = 5721176 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,476,251 reads read : 20,952,502 reads written : 20,952,502 2020-04-15T20:33:18 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 10,431,235 reads read : 20,862,470 reads written : 20,862,470 spots read : 10,270,222 reads read : 20,540,444 reads written : 20,540,444 spots read : 10,304,272 reads read : 20,608,544 reads written : 20,608,544 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: 00:14:04 41481980 reads; of these: 41481980 (100.00%) were paired; of these: 35655218 (85.95%) aligned concordantly 0 times 4550459 (10.97%) aligned concordantly exactly 1 time 1276303 (3.08%) aligned concordantly >1 times ---- 35655218 pairs aligned concordantly 0 times; of these: 19209 (0.05%) aligned discordantly 1 time ---- 35636009 pairs aligned 0 times concordantly or discordantly; of these: 71272018 mates make up the pairs; of these: 69847779 (98.00%) aligned 0 times 546582 (0.77%) aligned exactly 1 time 877657 (1.23%) aligned >1 times 15.81% overall alignment rate Time searching: 00:14:04 Overall time: 00:14:04 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] 214874 / 5833398 = 0.0368 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 06:09:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.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 06:09:40: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:09:40: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:09:46: 1000000 INFO @ Thu, 16 Apr 2020 06:09:52: 2000000 INFO @ Thu, 16 Apr 2020 06:09:59: 3000000 INFO @ Thu, 16 Apr 2020 06:10:05: 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 06:10:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.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 06:10:10: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:10:10: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:10:12: 5000000 INFO @ Thu, 16 Apr 2020 06:10:16: 1000000 INFO @ Thu, 16 Apr 2020 06:10:19: 6000000 INFO @ Thu, 16 Apr 2020 06:10:22: 2000000 INFO @ Thu, 16 Apr 2020 06:10:26: 7000000 INFO @ Thu, 16 Apr 2020 06:10:29: 3000000 INFO @ Thu, 16 Apr 2020 06:10:33: 8000000 INFO @ Thu, 16 Apr 2020 06:10:35: 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 06:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.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 06:10:40: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:10:40: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:10:40: 9000000 INFO @ Thu, 16 Apr 2020 06:10:42: 5000000 INFO @ Thu, 16 Apr 2020 06:10:46: 1000000 INFO @ Thu, 16 Apr 2020 06:10:47: 10000000 INFO @ Thu, 16 Apr 2020 06:10:48: 6000000 INFO @ Thu, 16 Apr 2020 06:10:52: 2000000 INFO @ Thu, 16 Apr 2020 06:10:54: 11000000 INFO @ Thu, 16 Apr 2020 06:10:54: 7000000 INFO @ Thu, 16 Apr 2020 06:10:59: 3000000 INFO @ Thu, 16 Apr 2020 06:11:01: 8000000 INFO @ Thu, 16 Apr 2020 06:11:01: 12000000 INFO @ Thu, 16 Apr 2020 06:11:05: 4000000 INFO @ Thu, 16 Apr 2020 06:11:06: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 06:11:06: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 06:11:06: #1 total tags in treatment: 5612007 INFO @ Thu, 16 Apr 2020 06:11:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:11:06: #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 06:11:06: #1 tags after filtering in treatment: 4796331 INFO @ Thu, 16 Apr 2020 06:11:06: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 06:11:06: #1 finished! INFO @ Thu, 16 Apr 2020 06:11:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:11:06: #2 number of paired peaks: 4633 INFO @ Thu, 16 Apr 2020 06:11:06: start model_add_line... INFO @ Thu, 16 Apr 2020 06:11:06: start X-correlation... INFO @ Thu, 16 Apr 2020 06:11:06: end of X-cor INFO @ Thu, 16 Apr 2020 06:11:06: #2 finished! INFO @ Thu, 16 Apr 2020 06:11:06: #2 predicted fragment length is 145 bps INFO @ Thu, 16 Apr 2020 06:11:06: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 16 Apr 2020 06:11:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.05_model.r INFO @ Thu, 16 Apr 2020 06:11:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:11:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:11:07: 9000000 INFO @ Thu, 16 Apr 2020 06:11:12: 5000000 INFO @ Thu, 16 Apr 2020 06:11:13: 10000000 INFO @ Thu, 16 Apr 2020 06:11:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:11:18: 6000000 INFO @ Thu, 16 Apr 2020 06:11:20: 11000000 INFO @ Thu, 16 Apr 2020 06:11:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:11:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:11:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.05_summits.bed INFO @ Thu, 16 Apr 2020 06:11:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6669 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:11:24: 7000000 INFO @ Thu, 16 Apr 2020 06:11:25: 12000000 INFO @ Thu, 16 Apr 2020 06:11:30: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 06:11:30: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 06:11:30: #1 total tags in treatment: 5612007 INFO @ Thu, 16 Apr 2020 06:11:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:11:30: #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 06:11:30: #1 tags after filtering in treatment: 4796331 INFO @ Thu, 16 Apr 2020 06:11:30: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 06:11:30: #1 finished! INFO @ Thu, 16 Apr 2020 06:11:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:11:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:11:30: 8000000 INFO @ Thu, 16 Apr 2020 06:11:30: #2 number of paired peaks: 4633 INFO @ Thu, 16 Apr 2020 06:11:30: start model_add_line... INFO @ Thu, 16 Apr 2020 06:11:30: start X-correlation... INFO @ Thu, 16 Apr 2020 06:11:30: end of X-cor INFO @ Thu, 16 Apr 2020 06:11:30: #2 finished! INFO @ Thu, 16 Apr 2020 06:11:30: #2 predicted fragment length is 145 bps INFO @ Thu, 16 Apr 2020 06:11:30: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 16 Apr 2020 06:11:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.10_model.r INFO @ Thu, 16 Apr 2020 06:11:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:11:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:11:36: 9000000 INFO @ Thu, 16 Apr 2020 06:11:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:11:41: 10000000 INFO @ Thu, 16 Apr 2020 06:11:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:11:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:11:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.10_summits.bed INFO @ Thu, 16 Apr 2020 06:11:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3093 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:11:47: 11000000 INFO @ Thu, 16 Apr 2020 06:11:52: 12000000 INFO @ Thu, 16 Apr 2020 06:11:55: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 06:11:55: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 06:11:55: #1 total tags in treatment: 5612007 INFO @ Thu, 16 Apr 2020 06:11:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:11:55: #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 06:11:56: #1 tags after filtering in treatment: 4796331 INFO @ Thu, 16 Apr 2020 06:11:56: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 06:11:56: #1 finished! INFO @ Thu, 16 Apr 2020 06:11:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:11:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:11:56: #2 number of paired peaks: 4633 INFO @ Thu, 16 Apr 2020 06:11:56: start model_add_line... INFO @ Thu, 16 Apr 2020 06:11:56: start X-correlation... INFO @ Thu, 16 Apr 2020 06:11:56: end of X-cor INFO @ Thu, 16 Apr 2020 06:11:56: #2 finished! INFO @ Thu, 16 Apr 2020 06:11:56: #2 predicted fragment length is 145 bps INFO @ Thu, 16 Apr 2020 06:11:56: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 16 Apr 2020 06:11:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.20_model.r INFO @ Thu, 16 Apr 2020 06:11:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:11:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:12:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762286/SRX6762286.20_summits.bed INFO @ Thu, 16 Apr 2020 06:12:13: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (848 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。