Job ID = 5720805 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T16:36:45 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 ) 2020-04-15T16:36:45 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 : 15,188,368 reads read : 30,376,736 reads written : 30,376,736 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: 00:38:22 15188368 reads; of these: 15188368 (100.00%) were paired; of these: 2450750 (16.14%) aligned concordantly 0 times 10816922 (71.22%) aligned concordantly exactly 1 time 1920696 (12.65%) aligned concordantly >1 times ---- 2450750 pairs aligned concordantly 0 times; of these: 91916 (3.75%) aligned discordantly 1 time ---- 2358834 pairs aligned 0 times concordantly or discordantly; of these: 4717668 mates make up the pairs; of these: 3480993 (73.79%) aligned 0 times 492458 (10.44%) aligned exactly 1 time 744217 (15.78%) aligned >1 times 88.54% overall alignment rate Time searching: 00:38:22 Overall time: 00:38:22 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] 3820543 / 12811234 = 0.2982 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 02:30:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.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 02:30:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:30:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:30:51: 1000000 INFO @ Thu, 16 Apr 2020 02:30:56: 2000000 INFO @ Thu, 16 Apr 2020 02:31:01: 3000000 INFO @ Thu, 16 Apr 2020 02:31:05: 4000000 INFO @ Thu, 16 Apr 2020 02:31:10: 5000000 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 02:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.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 02:31:15: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:31:15: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:31:15: 6000000 INFO @ Thu, 16 Apr 2020 02:31:20: 1000000 INFO @ Thu, 16 Apr 2020 02:31:20: 7000000 INFO @ Thu, 16 Apr 2020 02:31:24: 2000000 INFO @ Thu, 16 Apr 2020 02:31:24: 8000000 INFO @ Thu, 16 Apr 2020 02:31:29: 3000000 INFO @ Thu, 16 Apr 2020 02:31:29: 9000000 INFO @ Thu, 16 Apr 2020 02:31:34: 4000000 INFO @ Thu, 16 Apr 2020 02:31:34: 10000000 INFO @ Thu, 16 Apr 2020 02:31:39: 5000000 INFO @ Thu, 16 Apr 2020 02:31:39: 11000000 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 02:31:43: 6000000 INFO @ Thu, 16 Apr 2020 02:31:44: 12000000 INFO @ Thu, 16 Apr 2020 02:31:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.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 02:31:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:31:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:31:48: 7000000 INFO @ Thu, 16 Apr 2020 02:31:48: 13000000 INFO @ Thu, 16 Apr 2020 02:31:49: 1000000 INFO @ Thu, 16 Apr 2020 02:31:53: 8000000 INFO @ Thu, 16 Apr 2020 02:31:53: 14000000 INFO @ Thu, 16 Apr 2020 02:31:54: 2000000 INFO @ Thu, 16 Apr 2020 02:31:58: 9000000 INFO @ Thu, 16 Apr 2020 02:31:58: 15000000 INFO @ Thu, 16 Apr 2020 02:31:59: 3000000 INFO @ Thu, 16 Apr 2020 02:32:03: 10000000 INFO @ Thu, 16 Apr 2020 02:32:03: 16000000 INFO @ Thu, 16 Apr 2020 02:32:04: 4000000 INFO @ Thu, 16 Apr 2020 02:32:07: 11000000 INFO @ Thu, 16 Apr 2020 02:32:07: 17000000 INFO @ Thu, 16 Apr 2020 02:32:08: 5000000 INFO @ Thu, 16 Apr 2020 02:32:12: 12000000 INFO @ Thu, 16 Apr 2020 02:32:12: 18000000 INFO @ Thu, 16 Apr 2020 02:32:13: 6000000 INFO @ Thu, 16 Apr 2020 02:32:17: 13000000 INFO @ Thu, 16 Apr 2020 02:32:17: 19000000 INFO @ Thu, 16 Apr 2020 02:32:18: 7000000 INFO @ Thu, 16 Apr 2020 02:32:18: #1 tag size is determined as 78 bps INFO @ Thu, 16 Apr 2020 02:32:18: #1 tag size = 78 INFO @ Thu, 16 Apr 2020 02:32:18: #1 total tags in treatment: 8929255 INFO @ Thu, 16 Apr 2020 02:32:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:32:18: #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 02:32:19: #1 tags after filtering in treatment: 7469380 INFO @ Thu, 16 Apr 2020 02:32:19: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 02:32:19: #1 finished! INFO @ Thu, 16 Apr 2020 02:32:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:32:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:32:19: #2 number of paired peaks: 5401 INFO @ Thu, 16 Apr 2020 02:32:19: start model_add_line... INFO @ Thu, 16 Apr 2020 02:32:19: start X-correlation... INFO @ Thu, 16 Apr 2020 02:32:19: end of X-cor INFO @ Thu, 16 Apr 2020 02:32:19: #2 finished! INFO @ Thu, 16 Apr 2020 02:32:19: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 02:32:19: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 02:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.05_model.r INFO @ Thu, 16 Apr 2020 02:32:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:32:22: 14000000 INFO @ Thu, 16 Apr 2020 02:32:23: 8000000 INFO @ Thu, 16 Apr 2020 02:32:26: 15000000 INFO @ Thu, 16 Apr 2020 02:32:28: 9000000 INFO @ Thu, 16 Apr 2020 02:32:31: 16000000 INFO @ Thu, 16 Apr 2020 02:32:33: 10000000 INFO @ Thu, 16 Apr 2020 02:32:36: 17000000 INFO @ Thu, 16 Apr 2020 02:32:37: 11000000 INFO @ Thu, 16 Apr 2020 02:32:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:32:41: 18000000 INFO @ Thu, 16 Apr 2020 02:32:42: 12000000 INFO @ Thu, 16 Apr 2020 02:32:46: 19000000 INFO @ Thu, 16 Apr 2020 02:32:47: #1 tag size is determined as 78 bps INFO @ Thu, 16 Apr 2020 02:32:47: #1 tag size = 78 INFO @ Thu, 16 Apr 2020 02:32:47: #1 total tags in treatment: 8929255 INFO @ Thu, 16 Apr 2020 02:32:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:32:47: #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 02:32:47: #1 tags after filtering in treatment: 7469380 INFO @ Thu, 16 Apr 2020 02:32:47: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 02:32:47: #1 finished! INFO @ Thu, 16 Apr 2020 02:32:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:32:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:32:47: 13000000 INFO @ Thu, 16 Apr 2020 02:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.05_summits.bed INFO @ Thu, 16 Apr 2020 02:32:47: Done! INFO @ Thu, 16 Apr 2020 02:32:48: #2 number of paired peaks: 5401 INFO @ Thu, 16 Apr 2020 02:32:48: start model_add_line... INFO @ Thu, 16 Apr 2020 02:32:48: start X-correlation... INFO @ Thu, 16 Apr 2020 02:32:48: end of X-cor INFO @ Thu, 16 Apr 2020 02:32:48: #2 finished! INFO @ Thu, 16 Apr 2020 02:32:48: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 02:32:48: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 02:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.10_model.r INFO @ Thu, 16 Apr 2020 02:32:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:32:48: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7749 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:32:52: 14000000 INFO @ Thu, 16 Apr 2020 02:32:56: 15000000 INFO @ Thu, 16 Apr 2020 02:33:01: 16000000 INFO @ Thu, 16 Apr 2020 02:33:06: 17000000 INFO @ Thu, 16 Apr 2020 02:33:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:33:11: 18000000 INFO @ Thu, 16 Apr 2020 02:33:15: 19000000 INFO @ Thu, 16 Apr 2020 02:33:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:33:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:33:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.10_summits.bed INFO @ Thu, 16 Apr 2020 02:33:16: Done! INFO @ Thu, 16 Apr 2020 02:33:17: #1 tag size is determined as 78 bps INFO @ Thu, 16 Apr 2020 02:33:17: #1 tag size = 78 INFO @ Thu, 16 Apr 2020 02:33:17: #1 total tags in treatment: 8929255 INFO @ Thu, 16 Apr 2020 02:33:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:33:17: #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 02:33:17: #1 tags after filtering in treatment: 7469380 INFO @ Thu, 16 Apr 2020 02:33:17: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 02:33:17: #1 finished! INFO @ Thu, 16 Apr 2020 02:33:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:33:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:33:17: #2 number of paired peaks: 5401 INFO @ Thu, 16 Apr 2020 02:33:17: start model_add_line... INFO @ Thu, 16 Apr 2020 02:33:18: start X-correlation... INFO @ Thu, 16 Apr 2020 02:33:18: end of X-cor INFO @ Thu, 16 Apr 2020 02:33:18: #2 finished! INFO @ Thu, 16 Apr 2020 02:33:18: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 02:33:18: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 02:33:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.20_model.r INFO @ Thu, 16 Apr 2020 02:33:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:33:18: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6304 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:33:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:33:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:33:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:33:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309715/SRX5309715.20_summits.bed INFO @ Thu, 16 Apr 2020 02:33:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4711 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。