Job ID = 5721154 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T20:22:10 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 ) 2020-04-15T20:22:10 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 : 15,197,900 reads read : 30,395,800 reads written : 30,395,800 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: 00:21:51 15197900 reads; of these: 15197900 (100.00%) were paired; of these: 3802836 (25.02%) aligned concordantly 0 times 9272795 (61.01%) aligned concordantly exactly 1 time 2122269 (13.96%) aligned concordantly >1 times ---- 3802836 pairs aligned concordantly 0 times; of these: 211579 (5.56%) aligned discordantly 1 time ---- 3591257 pairs aligned 0 times concordantly or discordantly; of these: 7182514 mates make up the pairs; of these: 6665651 (92.80%) aligned 0 times 267369 (3.72%) aligned exactly 1 time 249494 (3.47%) aligned >1 times 78.07% overall alignment rate Time searching: 00:21:51 Overall time: 00:21:51 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] 663587 / 11599038 = 0.0572 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 05:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.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 05:57:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:57:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:58:03: 1000000 INFO @ Thu, 16 Apr 2020 05:58:09: 2000000 INFO @ Thu, 16 Apr 2020 05:58:15: 3000000 INFO @ Thu, 16 Apr 2020 05:58:21: 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 05:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.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 05:58:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:58:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:58:28: 5000000 INFO @ Thu, 16 Apr 2020 05:58:32: 1000000 INFO @ Thu, 16 Apr 2020 05:58:34: 6000000 INFO @ Thu, 16 Apr 2020 05:58:38: 2000000 INFO @ Thu, 16 Apr 2020 05:58:41: 7000000 INFO @ Thu, 16 Apr 2020 05:58:43: 3000000 INFO @ Thu, 16 Apr 2020 05:58:48: 8000000 INFO @ Thu, 16 Apr 2020 05:58:49: 4000000 INFO @ Thu, 16 Apr 2020 05:58:54: 9000000 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 05:58:55: 5000000 INFO @ Thu, 16 Apr 2020 05:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.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 05:58:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:58:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:59:00: 6000000 INFO @ Thu, 16 Apr 2020 05:59:01: 10000000 INFO @ Thu, 16 Apr 2020 05:59:02: 1000000 INFO @ Thu, 16 Apr 2020 05:59:06: 7000000 INFO @ Thu, 16 Apr 2020 05:59:08: 11000000 INFO @ Thu, 16 Apr 2020 05:59:08: 2000000 INFO @ Thu, 16 Apr 2020 05:59:12: 8000000 INFO @ Thu, 16 Apr 2020 05:59:14: 3000000 INFO @ Thu, 16 Apr 2020 05:59:14: 12000000 INFO @ Thu, 16 Apr 2020 05:59:18: 9000000 INFO @ Thu, 16 Apr 2020 05:59:19: 4000000 INFO @ Thu, 16 Apr 2020 05:59:21: 13000000 INFO @ Thu, 16 Apr 2020 05:59:23: 10000000 INFO @ Thu, 16 Apr 2020 05:59:25: 5000000 INFO @ Thu, 16 Apr 2020 05:59:27: 14000000 INFO @ Thu, 16 Apr 2020 05:59:29: 11000000 INFO @ Thu, 16 Apr 2020 05:59:31: 6000000 INFO @ Thu, 16 Apr 2020 05:59:34: 15000000 INFO @ Thu, 16 Apr 2020 05:59:35: 12000000 INFO @ Thu, 16 Apr 2020 05:59:36: 7000000 INFO @ Thu, 16 Apr 2020 05:59:40: 16000000 INFO @ Thu, 16 Apr 2020 05:59:40: 13000000 INFO @ Thu, 16 Apr 2020 05:59:42: 8000000 INFO @ Thu, 16 Apr 2020 05:59:46: 14000000 INFO @ Thu, 16 Apr 2020 05:59:47: 17000000 INFO @ Thu, 16 Apr 2020 05:59:48: 9000000 INFO @ Thu, 16 Apr 2020 05:59:52: 15000000 INFO @ Thu, 16 Apr 2020 05:59:53: 18000000 INFO @ Thu, 16 Apr 2020 05:59:53: 10000000 INFO @ Thu, 16 Apr 2020 05:59:58: 16000000 INFO @ Thu, 16 Apr 2020 05:59:59: 11000000 INFO @ Thu, 16 Apr 2020 06:00:00: 19000000 INFO @ Thu, 16 Apr 2020 06:00:03: 17000000 INFO @ Thu, 16 Apr 2020 06:00:05: 12000000 INFO @ Thu, 16 Apr 2020 06:00:06: 20000000 INFO @ Thu, 16 Apr 2020 06:00:09: 18000000 INFO @ Thu, 16 Apr 2020 06:00:11: 13000000 INFO @ Thu, 16 Apr 2020 06:00:13: 21000000 INFO @ Thu, 16 Apr 2020 06:00:15: 19000000 INFO @ Thu, 16 Apr 2020 06:00:16: 14000000 INFO @ Thu, 16 Apr 2020 06:00:19: 22000000 INFO @ Thu, 16 Apr 2020 06:00:21: 20000000 INFO @ Thu, 16 Apr 2020 06:00:22: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:00:22: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:00:22: #1 total tags in treatment: 10738128 INFO @ Thu, 16 Apr 2020 06:00:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:00:22: #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 06:00:22: 15000000 INFO @ Thu, 16 Apr 2020 06:00:22: #1 tags after filtering in treatment: 9024335 INFO @ Thu, 16 Apr 2020 06:00:22: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 06:00:22: #1 finished! INFO @ Thu, 16 Apr 2020 06:00:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:00:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:00:23: #2 number of paired peaks: 4591 INFO @ Thu, 16 Apr 2020 06:00:23: start model_add_line... INFO @ Thu, 16 Apr 2020 06:00:23: start X-correlation... INFO @ Thu, 16 Apr 2020 06:00:23: end of X-cor INFO @ Thu, 16 Apr 2020 06:00:23: #2 finished! INFO @ Thu, 16 Apr 2020 06:00:23: #2 predicted fragment length is 176 bps INFO @ Thu, 16 Apr 2020 06:00:23: #2 alternative fragment length(s) may be 176 bps INFO @ Thu, 16 Apr 2020 06:00:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.05_model.r INFO @ Thu, 16 Apr 2020 06:00:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:00:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:00:26: 21000000 INFO @ Thu, 16 Apr 2020 06:00:28: 16000000 INFO @ Thu, 16 Apr 2020 06:00:32: 22000000 INFO @ Thu, 16 Apr 2020 06:00:33: 17000000 INFO @ Thu, 16 Apr 2020 06:00:34: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:00:34: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:00:34: #1 total tags in treatment: 10738128 INFO @ Thu, 16 Apr 2020 06:00:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:00:34: #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 06:00:34: #1 tags after filtering in treatment: 9024335 INFO @ Thu, 16 Apr 2020 06:00:34: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 06:00:34: #1 finished! INFO @ Thu, 16 Apr 2020 06:00:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:00:35: #2 number of paired peaks: 4591 INFO @ Thu, 16 Apr 2020 06:00:35: start model_add_line... INFO @ Thu, 16 Apr 2020 06:00:35: start X-correlation... INFO @ Thu, 16 Apr 2020 06:00:35: end of X-cor INFO @ Thu, 16 Apr 2020 06:00:35: #2 finished! INFO @ Thu, 16 Apr 2020 06:00:35: #2 predicted fragment length is 176 bps INFO @ Thu, 16 Apr 2020 06:00:35: #2 alternative fragment length(s) may be 176 bps INFO @ Thu, 16 Apr 2020 06:00:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.10_model.r INFO @ Thu, 16 Apr 2020 06:00:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:00:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:00:39: 18000000 INFO @ Thu, 16 Apr 2020 06:00:44: 19000000 INFO @ Thu, 16 Apr 2020 06:00:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:00:49: 20000000 INFO @ Thu, 16 Apr 2020 06:00:54: 21000000 INFO @ Thu, 16 Apr 2020 06:00:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:00:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:00:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.05_summits.bed INFO @ Thu, 16 Apr 2020 06:00:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8835 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:01:00: 22000000 INFO @ Thu, 16 Apr 2020 06:01:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:01:02: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:01:02: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:01:02: #1 total tags in treatment: 10738128 INFO @ Thu, 16 Apr 2020 06:01:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:01:02: #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 06:01:02: #1 tags after filtering in treatment: 9024335 INFO @ Thu, 16 Apr 2020 06:01:02: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 06:01:02: #1 finished! INFO @ Thu, 16 Apr 2020 06:01:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:01:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:01:03: #2 number of paired peaks: 4591 INFO @ Thu, 16 Apr 2020 06:01:03: start model_add_line... INFO @ Thu, 16 Apr 2020 06:01:03: start X-correlation... INFO @ Thu, 16 Apr 2020 06:01:03: end of X-cor INFO @ Thu, 16 Apr 2020 06:01:03: #2 finished! INFO @ Thu, 16 Apr 2020 06:01:03: #2 predicted fragment length is 176 bps INFO @ Thu, 16 Apr 2020 06:01:03: #2 alternative fragment length(s) may be 176 bps INFO @ Thu, 16 Apr 2020 06:01:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.20_model.r INFO @ Thu, 16 Apr 2020 06:01:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:01:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:01:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:01:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:01:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.10_summits.bed INFO @ Thu, 16 Apr 2020 06:01:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7013 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:01:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:01:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:01:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:01:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708292/SRX6708292.20_summits.bed INFO @ Thu, 16 Apr 2020 06:01:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5314 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。