Job ID = 1294305 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T21:18:37 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 ) 2019-06-02T21:18:37 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 ) 2019-06-02T21:18:37 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 ) 2019-06-02T21:20:56 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 : 18,371,422 reads read : 18,371,422 reads written : 18,371,422 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:10:15 18371422 reads; of these: 18371422 (100.00%) were unpaired; of these: 444919 (2.42%) aligned 0 times 12260971 (66.74%) aligned exactly 1 time 5665532 (30.84%) aligned >1 times 97.58% overall alignment rate Time searching: 00:10:15 Overall time: 00:10:15 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 8 files... [bam_rmdupse_core] 1688140 / 17926503 = 0.0942 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 06:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.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 @ Mon, 03 Jun 2019 06:38:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:38:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.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 @ Mon, 03 Jun 2019 06:38:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:38:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.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 @ Mon, 03 Jun 2019 06:38:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:38:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:38:55: 1000000 INFO @ Mon, 03 Jun 2019 06:38:56: 1000000 INFO @ Mon, 03 Jun 2019 06:38:58: 1000000 INFO @ Mon, 03 Jun 2019 06:39:05: 2000000 INFO @ Mon, 03 Jun 2019 06:39:06: 2000000 INFO @ Mon, 03 Jun 2019 06:39:10: 2000000 INFO @ Mon, 03 Jun 2019 06:39:13: 3000000 INFO @ Mon, 03 Jun 2019 06:39:15: 3000000 INFO @ Mon, 03 Jun 2019 06:39:21: 3000000 INFO @ Mon, 03 Jun 2019 06:39:22: 4000000 INFO @ Mon, 03 Jun 2019 06:39:25: 4000000 INFO @ Mon, 03 Jun 2019 06:39:32: 5000000 INFO @ Mon, 03 Jun 2019 06:39:32: 4000000 INFO @ Mon, 03 Jun 2019 06:39:35: 5000000 INFO @ Mon, 03 Jun 2019 06:39:41: 6000000 INFO @ Mon, 03 Jun 2019 06:39:44: 5000000 INFO @ Mon, 03 Jun 2019 06:39:44: 6000000 INFO @ Mon, 03 Jun 2019 06:39:50: 7000000 INFO @ Mon, 03 Jun 2019 06:39:53: 7000000 INFO @ Mon, 03 Jun 2019 06:39:55: 6000000 INFO @ Mon, 03 Jun 2019 06:39:59: 8000000 INFO @ Mon, 03 Jun 2019 06:40:03: 8000000 INFO @ Mon, 03 Jun 2019 06:40:06: 7000000 INFO @ Mon, 03 Jun 2019 06:40:08: 9000000 INFO @ Mon, 03 Jun 2019 06:40:12: 9000000 INFO @ Mon, 03 Jun 2019 06:40:17: 10000000 INFO @ Mon, 03 Jun 2019 06:40:17: 8000000 INFO @ Mon, 03 Jun 2019 06:40:21: 10000000 INFO @ Mon, 03 Jun 2019 06:40:26: 11000000 INFO @ Mon, 03 Jun 2019 06:40:29: 9000000 INFO @ Mon, 03 Jun 2019 06:40:31: 11000000 INFO @ Mon, 03 Jun 2019 06:40:35: 12000000 INFO @ Mon, 03 Jun 2019 06:40:40: 10000000 INFO @ Mon, 03 Jun 2019 06:40:40: 12000000 INFO @ Mon, 03 Jun 2019 06:40:43: 13000000 INFO @ Mon, 03 Jun 2019 06:40:50: 13000000 INFO @ Mon, 03 Jun 2019 06:40:51: 11000000 INFO @ Mon, 03 Jun 2019 06:40:53: 14000000 INFO @ Mon, 03 Jun 2019 06:41:00: 14000000 INFO @ Mon, 03 Jun 2019 06:41:03: 12000000 INFO @ Mon, 03 Jun 2019 06:41:03: 15000000 INFO @ Mon, 03 Jun 2019 06:41:09: 15000000 INFO @ Mon, 03 Jun 2019 06:41:12: 16000000 INFO @ Mon, 03 Jun 2019 06:41:14: 13000000 INFO @ Mon, 03 Jun 2019 06:41:14: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:41:14: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:41:14: #1 total tags in treatment: 16238363 INFO @ Mon, 03 Jun 2019 06:41:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:41:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:41:15: #1 tags after filtering in treatment: 16238363 INFO @ Mon, 03 Jun 2019 06:41:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:41:15: #1 finished! INFO @ Mon, 03 Jun 2019 06:41:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:41:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:41:16: #2 number of paired peaks: 942 WARNING @ Mon, 03 Jun 2019 06:41:16: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Mon, 03 Jun 2019 06:41:16: start model_add_line... INFO @ Mon, 03 Jun 2019 06:41:16: start X-correlation... INFO @ Mon, 03 Jun 2019 06:41:16: end of X-cor INFO @ Mon, 03 Jun 2019 06:41:16: #2 finished! INFO @ Mon, 03 Jun 2019 06:41:16: #2 predicted fragment length is 161 bps INFO @ Mon, 03 Jun 2019 06:41:16: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 03 Jun 2019 06:41:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.20_model.r INFO @ Mon, 03 Jun 2019 06:41:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:41:18: 16000000 INFO @ Mon, 03 Jun 2019 06:41:21: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:41:21: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:41:21: #1 total tags in treatment: 16238363 INFO @ Mon, 03 Jun 2019 06:41:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:41:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:41:21: #1 tags after filtering in treatment: 16238363 INFO @ Mon, 03 Jun 2019 06:41:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:41:21: #1 finished! INFO @ Mon, 03 Jun 2019 06:41:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:41:23: #2 number of paired peaks: 942 WARNING @ Mon, 03 Jun 2019 06:41:23: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Mon, 03 Jun 2019 06:41:23: start model_add_line... INFO @ Mon, 03 Jun 2019 06:41:23: start X-correlation... INFO @ Mon, 03 Jun 2019 06:41:23: end of X-cor INFO @ Mon, 03 Jun 2019 06:41:23: #2 finished! INFO @ Mon, 03 Jun 2019 06:41:23: #2 predicted fragment length is 161 bps INFO @ Mon, 03 Jun 2019 06:41:23: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 03 Jun 2019 06:41:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.05_model.r INFO @ Mon, 03 Jun 2019 06:41:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:41:25: 14000000 INFO @ Mon, 03 Jun 2019 06:41:36: 15000000 INFO @ Mon, 03 Jun 2019 06:41:46: 16000000 INFO @ Mon, 03 Jun 2019 06:41:49: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:41:49: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:41:49: #1 total tags in treatment: 16238363 INFO @ Mon, 03 Jun 2019 06:41:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:41:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:41:49: #1 tags after filtering in treatment: 16238363 INFO @ Mon, 03 Jun 2019 06:41:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:41:49: #1 finished! INFO @ Mon, 03 Jun 2019 06:41:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:41:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:41:51: #2 number of paired peaks: 942 WARNING @ Mon, 03 Jun 2019 06:41:51: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Mon, 03 Jun 2019 06:41:51: start model_add_line... INFO @ Mon, 03 Jun 2019 06:41:51: start X-correlation... INFO @ Mon, 03 Jun 2019 06:41:51: end of X-cor INFO @ Mon, 03 Jun 2019 06:41:51: #2 finished! INFO @ Mon, 03 Jun 2019 06:41:51: #2 predicted fragment length is 161 bps INFO @ Mon, 03 Jun 2019 06:41:51: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 03 Jun 2019 06:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.10_model.r INFO @ Mon, 03 Jun 2019 06:41:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:42:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:42:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:42:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:42:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:42:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.20_summits.bed INFO @ Mon, 03 Jun 2019 06:42:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1619 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:42:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:42:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:42:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.05_summits.bed INFO @ Mon, 03 Jun 2019 06:42:31: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4189 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:42:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:42:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422635/SRX2422635.10_summits.bed INFO @ Mon, 03 Jun 2019 06:43:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2756 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。