Job ID = 3785862 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:36:06 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 ) 2019-11-01T05:36:12 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 ) 2019-11-01T05:36:40 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 ) 2019-11-01T05:36:40 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 ) 2019-11-01T05:36:40 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 : 6,533,000 reads read : 6,533,000 reads written : 6,533,000 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: 00:02:29 6533000 reads; of these: 6533000 (100.00%) were unpaired; of these: 469668 (7.19%) aligned 0 times 3944656 (60.38%) aligned exactly 1 time 2118676 (32.43%) aligned >1 times 92.81% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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_rmdupse_core] 354153 / 6063332 = 0.0584 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 14:43:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.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 @ Fri, 01 Nov 2019 14:43:02: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:43:02: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:43:09: 1000000 INFO @ Fri, 01 Nov 2019 14:43:16: 2000000 INFO @ Fri, 01 Nov 2019 14:43:23: 3000000 INFO @ Fri, 01 Nov 2019 14:43:31: 4000000 INFO @ Fri, 01 Nov 2019 14:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.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 @ Fri, 01 Nov 2019 14:43:31: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:43:31: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:43:38: 5000000 INFO @ Fri, 01 Nov 2019 14:43:42: 1000000 INFO @ Fri, 01 Nov 2019 14:43:43: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:43:43: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:43:43: #1 total tags in treatment: 5709179 INFO @ Fri, 01 Nov 2019 14:43:43: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:43:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:43:43: #1 tags after filtering in treatment: 5709179 INFO @ Fri, 01 Nov 2019 14:43:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:43:43: #1 finished! INFO @ Fri, 01 Nov 2019 14:43:43: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:43:44: #2 number of paired peaks: 1717 INFO @ Fri, 01 Nov 2019 14:43:44: start model_add_line... INFO @ Fri, 01 Nov 2019 14:43:44: start X-correlation... INFO @ Fri, 01 Nov 2019 14:43:44: end of X-cor INFO @ Fri, 01 Nov 2019 14:43:44: #2 finished! INFO @ Fri, 01 Nov 2019 14:43:44: #2 predicted fragment length is 143 bps INFO @ Fri, 01 Nov 2019 14:43:44: #2 alternative fragment length(s) may be 4,143 bps INFO @ Fri, 01 Nov 2019 14:43:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.05_model.r INFO @ Fri, 01 Nov 2019 14:43:44: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:43:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:43:51: 2000000 BedGraph に変換中... INFO @ Fri, 01 Nov 2019 14:44:01: 3000000 INFO @ Fri, 01 Nov 2019 14:44:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.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 @ Fri, 01 Nov 2019 14:44:02: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:44:02: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:44:02: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:44:10: 4000000 INFO @ Fri, 01 Nov 2019 14:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.05_peaks.xls INFO @ Fri, 01 Nov 2019 14:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.05_summits.bed INFO @ Fri, 01 Nov 2019 14:44:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2019 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:44:13: 1000000 INFO @ Fri, 01 Nov 2019 14:44:20: 5000000 INFO @ Fri, 01 Nov 2019 14:44:24: 2000000 INFO @ Fri, 01 Nov 2019 14:44:27: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:44:27: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:44:27: #1 total tags in treatment: 5709179 INFO @ Fri, 01 Nov 2019 14:44:27: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:44:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:44:27: #1 tags after filtering in treatment: 5709179 INFO @ Fri, 01 Nov 2019 14:44:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:44:27: #1 finished! INFO @ Fri, 01 Nov 2019 14:44:27: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:44:27: #2 number of paired peaks: 1717 INFO @ Fri, 01 Nov 2019 14:44:27: start model_add_line... INFO @ Fri, 01 Nov 2019 14:44:27: start X-correlation... INFO @ Fri, 01 Nov 2019 14:44:27: end of X-cor INFO @ Fri, 01 Nov 2019 14:44:27: #2 finished! INFO @ Fri, 01 Nov 2019 14:44:27: #2 predicted fragment length is 143 bps INFO @ Fri, 01 Nov 2019 14:44:27: #2 alternative fragment length(s) may be 4,143 bps INFO @ Fri, 01 Nov 2019 14:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.10_model.r INFO @ Fri, 01 Nov 2019 14:44:28: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:44:34: 3000000 INFO @ Fri, 01 Nov 2019 14:44:44: 4000000 INFO @ Fri, 01 Nov 2019 14:44:46: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:44:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.10_peaks.xls INFO @ Fri, 01 Nov 2019 14:44:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:44:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.10_summits.bed INFO @ Fri, 01 Nov 2019 14:44:54: Done! INFO @ Fri, 01 Nov 2019 14:44:54: 5000000 pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (964 records, 4 fields): 221 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:45:01: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:45:01: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:45:01: #1 total tags in treatment: 5709179 INFO @ Fri, 01 Nov 2019 14:45:01: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:45:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:45:01: #1 tags after filtering in treatment: 5709179 INFO @ Fri, 01 Nov 2019 14:45:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:45:01: #1 finished! INFO @ Fri, 01 Nov 2019 14:45:01: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:45:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:45:02: #2 number of paired peaks: 1717 INFO @ Fri, 01 Nov 2019 14:45:02: start model_add_line... INFO @ Fri, 01 Nov 2019 14:45:02: start X-correlation... INFO @ Fri, 01 Nov 2019 14:45:02: end of X-cor INFO @ Fri, 01 Nov 2019 14:45:02: #2 finished! INFO @ Fri, 01 Nov 2019 14:45:02: #2 predicted fragment length is 143 bps INFO @ Fri, 01 Nov 2019 14:45:02: #2 alternative fragment length(s) may be 4,143 bps INFO @ Fri, 01 Nov 2019 14:45:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.20_model.r INFO @ Fri, 01 Nov 2019 14:45:02: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:45:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:45:20: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:45:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.20_peaks.xls INFO @ Fri, 01 Nov 2019 14:45:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:45:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5247955/SRX5247955.20_summits.bed INFO @ Fri, 01 Nov 2019 14:45:31: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (376 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。