Job ID = 1294115 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T19:54:12 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 ) 2019-06-02T20:06:11 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( ) 2019-06-02T20:06:11 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 : 29,943,013 reads read : 29,943,013 reads written : 29,943,013 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: 00:08:43 29943013 reads; of these: 29943013 (100.00%) were unpaired; of these: 2513017 (8.39%) aligned 0 times 22679963 (75.74%) aligned exactly 1 time 4750033 (15.86%) aligned >1 times 91.61% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 18727137 / 27429996 = 0.6827 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 05:28:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.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 05:28:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:28:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:28:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.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 05:28:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:28:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:28:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.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 05:28:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:28:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:28:12: 1000000 INFO @ Mon, 03 Jun 2019 05:28:13: 1000000 INFO @ Mon, 03 Jun 2019 05:28:15: 1000000 INFO @ Mon, 03 Jun 2019 05:28:20: 2000000 INFO @ Mon, 03 Jun 2019 05:28:21: 2000000 INFO @ Mon, 03 Jun 2019 05:28:25: 2000000 INFO @ Mon, 03 Jun 2019 05:28:28: 3000000 INFO @ Mon, 03 Jun 2019 05:28:28: 3000000 INFO @ Mon, 03 Jun 2019 05:28:35: 3000000 INFO @ Mon, 03 Jun 2019 05:28:36: 4000000 INFO @ Mon, 03 Jun 2019 05:28:36: 4000000 INFO @ Mon, 03 Jun 2019 05:28:44: 5000000 INFO @ Mon, 03 Jun 2019 05:28:44: 5000000 INFO @ Mon, 03 Jun 2019 05:28:45: 4000000 INFO @ Mon, 03 Jun 2019 05:28:52: 6000000 INFO @ Mon, 03 Jun 2019 05:28:52: 6000000 INFO @ Mon, 03 Jun 2019 05:28:55: 5000000 INFO @ Mon, 03 Jun 2019 05:29:00: 7000000 INFO @ Mon, 03 Jun 2019 05:29:01: 7000000 INFO @ Mon, 03 Jun 2019 05:29:05: 6000000 INFO @ Mon, 03 Jun 2019 05:29:08: 8000000 INFO @ Mon, 03 Jun 2019 05:29:09: 8000000 INFO @ Mon, 03 Jun 2019 05:29:13: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:29:13: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:29:13: #1 total tags in treatment: 8702859 INFO @ Mon, 03 Jun 2019 05:29:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:29:13: #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 05:29:14: #1 tags after filtering in treatment: 8702859 INFO @ Mon, 03 Jun 2019 05:29:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:29:14: #1 finished! INFO @ Mon, 03 Jun 2019 05:29:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:29:14: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:29:14: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:29:14: #1 total tags in treatment: 8702859 INFO @ Mon, 03 Jun 2019 05:29:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:29:14: #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 05:29:15: #1 tags after filtering in treatment: 8702859 INFO @ Mon, 03 Jun 2019 05:29:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:29:15: #1 finished! INFO @ Mon, 03 Jun 2019 05:29:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:29:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:29:15: #2 number of paired peaks: 3974 INFO @ Mon, 03 Jun 2019 05:29:15: start model_add_line... INFO @ Mon, 03 Jun 2019 05:29:15: start X-correlation... INFO @ Mon, 03 Jun 2019 05:29:15: end of X-cor INFO @ Mon, 03 Jun 2019 05:29:15: #2 finished! INFO @ Mon, 03 Jun 2019 05:29:15: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 05:29:15: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 05:29:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.05_model.r INFO @ Mon, 03 Jun 2019 05:29:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:29:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:29:16: #2 number of paired peaks: 3974 INFO @ Mon, 03 Jun 2019 05:29:16: start model_add_line... INFO @ Mon, 03 Jun 2019 05:29:16: start X-correlation... INFO @ Mon, 03 Jun 2019 05:29:16: end of X-cor INFO @ Mon, 03 Jun 2019 05:29:16: #2 finished! INFO @ Mon, 03 Jun 2019 05:29:16: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 05:29:16: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 05:29:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.10_model.r INFO @ Mon, 03 Jun 2019 05:29:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:29:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:29:16: 7000000 INFO @ Mon, 03 Jun 2019 05:29:26: 8000000 INFO @ Mon, 03 Jun 2019 05:29:33: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:29:33: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:29:33: #1 total tags in treatment: 8702859 INFO @ Mon, 03 Jun 2019 05:29:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:29:33: #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 05:29:34: #1 tags after filtering in treatment: 8702859 INFO @ Mon, 03 Jun 2019 05:29:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:29:34: #1 finished! INFO @ Mon, 03 Jun 2019 05:29:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:29:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:29:35: #2 number of paired peaks: 3974 INFO @ Mon, 03 Jun 2019 05:29:35: start model_add_line... INFO @ Mon, 03 Jun 2019 05:29:35: start X-correlation... INFO @ Mon, 03 Jun 2019 05:29:35: end of X-cor INFO @ Mon, 03 Jun 2019 05:29:35: #2 finished! INFO @ Mon, 03 Jun 2019 05:29:35: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 05:29:35: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 05:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.20_model.r INFO @ Mon, 03 Jun 2019 05:29:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:29:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:29:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:29:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:29:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:29:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.10_summits.bed INFO @ Mon, 03 Jun 2019 05:29:55: Done! INFO @ Mon, 03 Jun 2019 05:29:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:29:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.05_peaks.narrowPeak pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (12415 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:29:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.05_summits.bed INFO @ Mon, 03 Jun 2019 05:29:55: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (16140 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:30:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:30:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:30:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:30:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191907/SRX191907.20_summits.bed INFO @ Mon, 03 Jun 2019 05:30:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9161 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。