Job ID = 5790673 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:53:21 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 ) 2020-04-21T20:58:55 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 ) 2020-04-21T20:58:55 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 ) 2020-04-21T20:58:55 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 ) 2020-04-21T21:00:18 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 ) 2020-04-21T21:01:49 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 : 19,151,300 reads read : 19,151,300 reads written : 19,151,300 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:53 19151300 reads; of these: 19151300 (100.00%) were unpaired; of these: 3166539 (16.53%) aligned 0 times 9359594 (48.87%) aligned exactly 1 time 6625167 (34.59%) aligned >1 times 83.47% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1393359 / 15984761 = 0.0872 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 @ Wed, 22 Apr 2020 06:13:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:13:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:13:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:13:18: 1000000 INFO @ Wed, 22 Apr 2020 06:13:23: 2000000 INFO @ Wed, 22 Apr 2020 06:13:28: 3000000 INFO @ Wed, 22 Apr 2020 06:13:33: 4000000 INFO @ Wed, 22 Apr 2020 06:13:38: 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 @ Wed, 22 Apr 2020 06:13:43: 6000000 INFO @ Wed, 22 Apr 2020 06:13:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:13:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:13:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:13:48: 7000000 INFO @ Wed, 22 Apr 2020 06:13:50: 1000000 INFO @ Wed, 22 Apr 2020 06:13:54: 8000000 INFO @ Wed, 22 Apr 2020 06:13:56: 2000000 INFO @ Wed, 22 Apr 2020 06:13:59: 9000000 INFO @ Wed, 22 Apr 2020 06:14:03: 3000000 INFO @ Wed, 22 Apr 2020 06:14:05: 10000000 INFO @ Wed, 22 Apr 2020 06:14:09: 4000000 INFO @ Wed, 22 Apr 2020 06:14:10: 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 @ Wed, 22 Apr 2020 06:14:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:14:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:14:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:14:15: 5000000 INFO @ Wed, 22 Apr 2020 06:14:15: 12000000 INFO @ Wed, 22 Apr 2020 06:14:19: 1000000 INFO @ Wed, 22 Apr 2020 06:14:21: 13000000 INFO @ Wed, 22 Apr 2020 06:14:21: 6000000 INFO @ Wed, 22 Apr 2020 06:14:25: 2000000 INFO @ Wed, 22 Apr 2020 06:14:26: 14000000 INFO @ Wed, 22 Apr 2020 06:14:28: 7000000 INFO @ Wed, 22 Apr 2020 06:14:30: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:14:30: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:14:30: #1 total tags in treatment: 14591402 INFO @ Wed, 22 Apr 2020 06:14:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:14:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:14:30: #1 tags after filtering in treatment: 14591258 INFO @ Wed, 22 Apr 2020 06:14:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:14:30: #1 finished! INFO @ Wed, 22 Apr 2020 06:14:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:14:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:14:31: 3000000 INFO @ Wed, 22 Apr 2020 06:14:32: #2 number of paired peaks: 15060 INFO @ Wed, 22 Apr 2020 06:14:32: start model_add_line... INFO @ Wed, 22 Apr 2020 06:14:32: start X-correlation... INFO @ Wed, 22 Apr 2020 06:14:32: end of X-cor INFO @ Wed, 22 Apr 2020 06:14:32: #2 finished! INFO @ Wed, 22 Apr 2020 06:14:32: #2 predicted fragment length is 175 bps INFO @ Wed, 22 Apr 2020 06:14:32: #2 alternative fragment length(s) may be 41,175 bps INFO @ Wed, 22 Apr 2020 06:14:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.05_model.r INFO @ Wed, 22 Apr 2020 06:14:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:14:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:14:34: 8000000 INFO @ Wed, 22 Apr 2020 06:14:37: 4000000 INFO @ Wed, 22 Apr 2020 06:14:41: 9000000 INFO @ Wed, 22 Apr 2020 06:14:42: 5000000 INFO @ Wed, 22 Apr 2020 06:14:47: 10000000 INFO @ Wed, 22 Apr 2020 06:14:48: 6000000 INFO @ Wed, 22 Apr 2020 06:14:53: 7000000 INFO @ Wed, 22 Apr 2020 06:14:53: 11000000 INFO @ Wed, 22 Apr 2020 06:14:59: 8000000 INFO @ Wed, 22 Apr 2020 06:14:59: 12000000 INFO @ Wed, 22 Apr 2020 06:15:04: 9000000 INFO @ Wed, 22 Apr 2020 06:15:05: 13000000 INFO @ Wed, 22 Apr 2020 06:15:06: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:15:09: 10000000 INFO @ Wed, 22 Apr 2020 06:15:11: 14000000 INFO @ Wed, 22 Apr 2020 06:15:15: 11000000 INFO @ Wed, 22 Apr 2020 06:15:15: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:15:15: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:15:15: #1 total tags in treatment: 14591402 INFO @ Wed, 22 Apr 2020 06:15:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:15:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:15:16: #1 tags after filtering in treatment: 14591258 INFO @ Wed, 22 Apr 2020 06:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:15:16: #1 finished! INFO @ Wed, 22 Apr 2020 06:15:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:15:17: #2 number of paired peaks: 15060 INFO @ Wed, 22 Apr 2020 06:15:17: start model_add_line... INFO @ Wed, 22 Apr 2020 06:15:17: start X-correlation... INFO @ Wed, 22 Apr 2020 06:15:17: end of X-cor INFO @ Wed, 22 Apr 2020 06:15:17: #2 finished! INFO @ Wed, 22 Apr 2020 06:15:17: #2 predicted fragment length is 175 bps INFO @ Wed, 22 Apr 2020 06:15:17: #2 alternative fragment length(s) may be 41,175 bps INFO @ Wed, 22 Apr 2020 06:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.10_model.r INFO @ Wed, 22 Apr 2020 06:15:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:15:20: 12000000 INFO @ Wed, 22 Apr 2020 06:15:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:15:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:15:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.05_summits.bed INFO @ Wed, 22 Apr 2020 06:15:23: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (5304 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:15:25: 13000000 INFO @ Wed, 22 Apr 2020 06:15:31: 14000000 INFO @ Wed, 22 Apr 2020 06:15:34: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:15:34: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:15:34: #1 total tags in treatment: 14591402 INFO @ Wed, 22 Apr 2020 06:15:34: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:15:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:15:34: #1 tags after filtering in treatment: 14591258 INFO @ Wed, 22 Apr 2020 06:15:34: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:15:34: #1 finished! INFO @ Wed, 22 Apr 2020 06:15:34: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:15:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:15:36: #2 number of paired peaks: 15060 INFO @ Wed, 22 Apr 2020 06:15:36: start model_add_line... INFO @ Wed, 22 Apr 2020 06:15:36: start X-correlation... INFO @ Wed, 22 Apr 2020 06:15:36: end of X-cor INFO @ Wed, 22 Apr 2020 06:15:36: #2 finished! INFO @ Wed, 22 Apr 2020 06:15:36: #2 predicted fragment length is 175 bps INFO @ Wed, 22 Apr 2020 06:15:36: #2 alternative fragment length(s) may be 41,175 bps INFO @ Wed, 22 Apr 2020 06:15:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.20_model.r INFO @ Wed, 22 Apr 2020 06:15:36: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:15:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:15:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.10_summits.bed INFO @ Wed, 22 Apr 2020 06:16:08: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (943 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:16:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:16:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:16:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:16:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761708/SRX5761708.20_summits.bed INFO @ Wed, 22 Apr 2020 06:16:27: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。