Job ID = 1306924 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:02:03 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 ) 2019-06-03T13:02:03 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 ) 2019-06-03T13:02:03 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 ) 2019-06-03T13:02:53 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 ) 2019-06-03T13:03:50 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 : 14,216,384 reads read : 14,216,384 reads written : 14,216,384 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: 00:11:58 14216384 reads; of these: 14216384 (100.00%) were unpaired; of these: 224137 (1.58%) aligned 0 times 3154874 (22.19%) aligned exactly 1 time 10837373 (76.23%) aligned >1 times 98.42% overall alignment rate Time searching: 00:11:58 Overall time: 00:11:58 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] 2890491 / 13992247 = 0.2066 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 22:24:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.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 22:24:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.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 22:24:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.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 22:24:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:14: 1000000 INFO @ Mon, 03 Jun 2019 22:24:16: 1000000 INFO @ Mon, 03 Jun 2019 22:24:16: 1000000 INFO @ Mon, 03 Jun 2019 22:24:21: 2000000 INFO @ Mon, 03 Jun 2019 22:24:25: 2000000 INFO @ Mon, 03 Jun 2019 22:24:26: 2000000 INFO @ Mon, 03 Jun 2019 22:24:28: 3000000 INFO @ Mon, 03 Jun 2019 22:24:34: 3000000 INFO @ Mon, 03 Jun 2019 22:24:34: 3000000 INFO @ Mon, 03 Jun 2019 22:24:35: 4000000 INFO @ Mon, 03 Jun 2019 22:24:41: 5000000 INFO @ Mon, 03 Jun 2019 22:24:42: 4000000 INFO @ Mon, 03 Jun 2019 22:24:42: 4000000 INFO @ Mon, 03 Jun 2019 22:24:48: 6000000 INFO @ Mon, 03 Jun 2019 22:24:50: 5000000 INFO @ Mon, 03 Jun 2019 22:24:51: 5000000 INFO @ Mon, 03 Jun 2019 22:24:55: 7000000 INFO @ Mon, 03 Jun 2019 22:24:59: 6000000 INFO @ Mon, 03 Jun 2019 22:24:59: 6000000 INFO @ Mon, 03 Jun 2019 22:25:01: 8000000 INFO @ Mon, 03 Jun 2019 22:25:07: 7000000 INFO @ Mon, 03 Jun 2019 22:25:08: 7000000 INFO @ Mon, 03 Jun 2019 22:25:08: 9000000 INFO @ Mon, 03 Jun 2019 22:25:15: 10000000 INFO @ Mon, 03 Jun 2019 22:25:15: 8000000 INFO @ Mon, 03 Jun 2019 22:25:16: 8000000 INFO @ Mon, 03 Jun 2019 22:25:22: 11000000 INFO @ Mon, 03 Jun 2019 22:25:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:25:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:25:23: #1 total tags in treatment: 11101756 INFO @ Mon, 03 Jun 2019 22:25:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:25:23: #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 22:25:23: #1 tags after filtering in treatment: 11101756 INFO @ Mon, 03 Jun 2019 22:25:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:25:23: #1 finished! INFO @ Mon, 03 Jun 2019 22:25:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:25:24: 9000000 INFO @ Mon, 03 Jun 2019 22:25:24: 9000000 INFO @ Mon, 03 Jun 2019 22:25:25: #2 number of paired peaks: 1982 INFO @ Mon, 03 Jun 2019 22:25:25: start model_add_line... INFO @ Mon, 03 Jun 2019 22:25:25: start X-correlation... INFO @ Mon, 03 Jun 2019 22:25:25: end of X-cor INFO @ Mon, 03 Jun 2019 22:25:25: #2 finished! INFO @ Mon, 03 Jun 2019 22:25:25: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 22:25:25: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 22:25:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.05_model.r WARNING @ Mon, 03 Jun 2019 22:25:25: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:25:25: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 22:25:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:25:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:25:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:25:32: 10000000 INFO @ Mon, 03 Jun 2019 22:25:33: 10000000 INFO @ Mon, 03 Jun 2019 22:25:41: 11000000 INFO @ Mon, 03 Jun 2019 22:25:41: 11000000 INFO @ Mon, 03 Jun 2019 22:25:42: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:25:42: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:25:42: #1 total tags in treatment: 11101756 INFO @ Mon, 03 Jun 2019 22:25:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:25:42: #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 22:25:42: #1 tags after filtering in treatment: 11101756 INFO @ Mon, 03 Jun 2019 22:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:25:42: #1 finished! INFO @ Mon, 03 Jun 2019 22:25:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:25:42: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:25:42: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:25:42: #1 total tags in treatment: 11101756 INFO @ Mon, 03 Jun 2019 22:25:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:25:42: #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 22:25:42: #1 tags after filtering in treatment: 11101756 INFO @ Mon, 03 Jun 2019 22:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:25:42: #1 finished! INFO @ Mon, 03 Jun 2019 22:25:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:25:43: #2 number of paired peaks: 1982 INFO @ Mon, 03 Jun 2019 22:25:43: start model_add_line... INFO @ Mon, 03 Jun 2019 22:25:43: start X-correlation... INFO @ Mon, 03 Jun 2019 22:25:43: end of X-cor INFO @ Mon, 03 Jun 2019 22:25:43: #2 finished! INFO @ Mon, 03 Jun 2019 22:25:43: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 22:25:43: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 22:25:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.20_model.r WARNING @ Mon, 03 Jun 2019 22:25:43: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:25:43: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 22:25:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:25:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:25:44: #2 number of paired peaks: 1982 INFO @ Mon, 03 Jun 2019 22:25:44: start model_add_line... INFO @ Mon, 03 Jun 2019 22:25:44: start X-correlation... INFO @ Mon, 03 Jun 2019 22:25:44: end of X-cor INFO @ Mon, 03 Jun 2019 22:25:44: #2 finished! INFO @ Mon, 03 Jun 2019 22:25:44: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 22:25:44: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 22:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.10_model.r WARNING @ Mon, 03 Jun 2019 22:25:44: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:25:44: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 22:25:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:25:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:25:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:26:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:26:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.05_summits.bed INFO @ Mon, 03 Jun 2019 22:26:11: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (10055 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:26:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:26:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.20_summits.bed INFO @ Mon, 03 Jun 2019 22:26:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1378 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:26:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:26:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:26:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511129/SRX511129.10_summits.bed INFO @ Mon, 03 Jun 2019 22:26:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2865 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。