Job ID = 1301478 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:56:44 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 ) 2019-06-03T11:03:45 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 ) 2019-06-03T11:03:45 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 ) 2019-06-03T11:03:45 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 ) 2019-06-03T11:03:45 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 : 23,418,085 reads read : 23,418,085 reads written : 23,418,085 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: 00:10:05 23418085 reads; of these: 23418085 (100.00%) were unpaired; of these: 1363169 (5.82%) aligned 0 times 11334198 (48.40%) aligned exactly 1 time 10720718 (45.78%) aligned >1 times 94.18% overall alignment rate Time searching: 00:10:05 Overall time: 00:10:05 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_rmdupse_core] 5154162 / 22054916 = 0.2337 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 20:22:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.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 20:22:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:22:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:22:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.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 20:22:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:22:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:22:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.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 20:22:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:22:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:22:39: 1000000 INFO @ Mon, 03 Jun 2019 20:22:40: 1000000 INFO @ Mon, 03 Jun 2019 20:22:40: 1000000 INFO @ Mon, 03 Jun 2019 20:22:47: 2000000 INFO @ Mon, 03 Jun 2019 20:22:48: 2000000 INFO @ Mon, 03 Jun 2019 20:22:48: 2000000 INFO @ Mon, 03 Jun 2019 20:22:54: 3000000 INFO @ Mon, 03 Jun 2019 20:22:55: 3000000 INFO @ Mon, 03 Jun 2019 20:22:56: 3000000 INFO @ Mon, 03 Jun 2019 20:23:02: 4000000 INFO @ Mon, 03 Jun 2019 20:23:02: 4000000 INFO @ Mon, 03 Jun 2019 20:23:03: 4000000 INFO @ Mon, 03 Jun 2019 20:23:09: 5000000 INFO @ Mon, 03 Jun 2019 20:23:09: 5000000 INFO @ Mon, 03 Jun 2019 20:23:10: 5000000 INFO @ Mon, 03 Jun 2019 20:23:16: 6000000 INFO @ Mon, 03 Jun 2019 20:23:17: 6000000 INFO @ Mon, 03 Jun 2019 20:23:17: 6000000 INFO @ Mon, 03 Jun 2019 20:23:23: 7000000 INFO @ Mon, 03 Jun 2019 20:23:24: 7000000 INFO @ Mon, 03 Jun 2019 20:23:24: 7000000 INFO @ Mon, 03 Jun 2019 20:23:30: 8000000 INFO @ Mon, 03 Jun 2019 20:23:30: 8000000 INFO @ Mon, 03 Jun 2019 20:23:32: 8000000 INFO @ Mon, 03 Jun 2019 20:23:37: 9000000 INFO @ Mon, 03 Jun 2019 20:23:37: 9000000 INFO @ Mon, 03 Jun 2019 20:23:39: 9000000 INFO @ Mon, 03 Jun 2019 20:23:44: 10000000 INFO @ Mon, 03 Jun 2019 20:23:45: 10000000 INFO @ Mon, 03 Jun 2019 20:23:47: 10000000 INFO @ Mon, 03 Jun 2019 20:23:51: 11000000 INFO @ Mon, 03 Jun 2019 20:23:52: 11000000 INFO @ Mon, 03 Jun 2019 20:23:54: 11000000 INFO @ Mon, 03 Jun 2019 20:23:58: 12000000 INFO @ Mon, 03 Jun 2019 20:23:59: 12000000 INFO @ Mon, 03 Jun 2019 20:24:02: 12000000 INFO @ Mon, 03 Jun 2019 20:24:05: 13000000 INFO @ Mon, 03 Jun 2019 20:24:06: 13000000 INFO @ Mon, 03 Jun 2019 20:24:09: 13000000 INFO @ Mon, 03 Jun 2019 20:24:12: 14000000 INFO @ Mon, 03 Jun 2019 20:24:12: 14000000 INFO @ Mon, 03 Jun 2019 20:24:16: 14000000 INFO @ Mon, 03 Jun 2019 20:24:19: 15000000 INFO @ Mon, 03 Jun 2019 20:24:19: 15000000 INFO @ Mon, 03 Jun 2019 20:24:24: 15000000 INFO @ Mon, 03 Jun 2019 20:24:26: 16000000 INFO @ Mon, 03 Jun 2019 20:24:27: 16000000 INFO @ Mon, 03 Jun 2019 20:24:32: 16000000 INFO @ Mon, 03 Jun 2019 20:24:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:24:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:24:32: #1 total tags in treatment: 16900754 INFO @ Mon, 03 Jun 2019 20:24:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:24:32: #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 20:24:33: #1 tags after filtering in treatment: 16900754 INFO @ Mon, 03 Jun 2019 20:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:24:33: #1 finished! INFO @ Mon, 03 Jun 2019 20:24:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:24:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:24:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:24:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:24:34: #1 total tags in treatment: 16900754 INFO @ Mon, 03 Jun 2019 20:24:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:24:34: #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 20:24:34: #2 number of paired peaks: 1292 INFO @ Mon, 03 Jun 2019 20:24:34: start model_add_line... INFO @ Mon, 03 Jun 2019 20:24:34: #1 tags after filtering in treatment: 16900754 INFO @ Mon, 03 Jun 2019 20:24:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:24:34: #1 finished! INFO @ Mon, 03 Jun 2019 20:24:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:24:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:24:34: start X-correlation... INFO @ Mon, 03 Jun 2019 20:24:34: end of X-cor INFO @ Mon, 03 Jun 2019 20:24:34: #2 finished! INFO @ Mon, 03 Jun 2019 20:24:34: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 20:24:34: #2 alternative fragment length(s) may be 4,215 bps INFO @ Mon, 03 Jun 2019 20:24:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.10_model.r INFO @ Mon, 03 Jun 2019 20:24:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:24:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:24:36: #2 number of paired peaks: 1292 INFO @ Mon, 03 Jun 2019 20:24:36: start model_add_line... INFO @ Mon, 03 Jun 2019 20:24:36: start X-correlation... INFO @ Mon, 03 Jun 2019 20:24:36: end of X-cor INFO @ Mon, 03 Jun 2019 20:24:36: #2 finished! INFO @ Mon, 03 Jun 2019 20:24:36: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 20:24:36: #2 alternative fragment length(s) may be 4,215 bps INFO @ Mon, 03 Jun 2019 20:24:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.05_model.r INFO @ Mon, 03 Jun 2019 20:24:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:24:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:24:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:24:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:24:39: #1 total tags in treatment: 16900754 INFO @ Mon, 03 Jun 2019 20:24:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:24:39: #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 20:24:39: #1 tags after filtering in treatment: 16900754 INFO @ Mon, 03 Jun 2019 20:24:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:24:39: #1 finished! INFO @ Mon, 03 Jun 2019 20:24:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:24:41: #2 number of paired peaks: 1292 INFO @ Mon, 03 Jun 2019 20:24:41: start model_add_line... INFO @ Mon, 03 Jun 2019 20:24:41: start X-correlation... INFO @ Mon, 03 Jun 2019 20:24:41: end of X-cor INFO @ Mon, 03 Jun 2019 20:24:41: #2 finished! INFO @ Mon, 03 Jun 2019 20:24:41: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 20:24:41: #2 alternative fragment length(s) may be 4,215 bps INFO @ Mon, 03 Jun 2019 20:24:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.20_model.r INFO @ Mon, 03 Jun 2019 20:24:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:24:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:25:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:25:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:25:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:25:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:25:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:25:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.10_summits.bed INFO @ Mon, 03 Jun 2019 20:25:51: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5541 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:25:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:25:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:25:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.05_summits.bed INFO @ Mon, 03 Jun 2019 20:25:53: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10424 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485217/SRX485217.20_summits.bed INFO @ Mon, 03 Jun 2019 20:25:57: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2495 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。