Job ID = 1293835 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:45:38 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 ) 2019-06-02T17:45:38 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 ) 2019-06-02T17:45:38 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 : 29,363,939 reads read : 29,363,939 reads written : 29,363,939 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: 00:00:01 Multiseed full-index search: 00:08:46 29363939 reads; of these: 29363939 (100.00%) were unpaired; of these: 5509321 (18.76%) aligned 0 times 16918970 (57.62%) aligned exactly 1 time 6935648 (23.62%) aligned >1 times 81.24% overall alignment rate Time searching: 00:08:47 Overall time: 00:08:47 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] 10398390 / 23854618 = 0.4359 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 03:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.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 03:05:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:05:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.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 03:05:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:05:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.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 03:05:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:05:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:05:50: 1000000 INFO @ Mon, 03 Jun 2019 03:05:50: 1000000 INFO @ Mon, 03 Jun 2019 03:05:52: 1000000 INFO @ Mon, 03 Jun 2019 03:05:58: 2000000 INFO @ Mon, 03 Jun 2019 03:05:58: 2000000 INFO @ Mon, 03 Jun 2019 03:06:02: 2000000 INFO @ Mon, 03 Jun 2019 03:06:06: 3000000 INFO @ Mon, 03 Jun 2019 03:06:06: 3000000 INFO @ Mon, 03 Jun 2019 03:06:11: 3000000 INFO @ Mon, 03 Jun 2019 03:06:14: 4000000 INFO @ Mon, 03 Jun 2019 03:06:14: 4000000 INFO @ Mon, 03 Jun 2019 03:06:20: 4000000 INFO @ Mon, 03 Jun 2019 03:06:21: 5000000 INFO @ Mon, 03 Jun 2019 03:06:22: 5000000 INFO @ Mon, 03 Jun 2019 03:06:29: 6000000 INFO @ Mon, 03 Jun 2019 03:06:30: 6000000 INFO @ Mon, 03 Jun 2019 03:06:30: 5000000 INFO @ Mon, 03 Jun 2019 03:06:36: 7000000 INFO @ Mon, 03 Jun 2019 03:06:37: 7000000 INFO @ Mon, 03 Jun 2019 03:06:39: 6000000 INFO @ Mon, 03 Jun 2019 03:06:43: 8000000 INFO @ Mon, 03 Jun 2019 03:06:45: 8000000 INFO @ Mon, 03 Jun 2019 03:06:49: 7000000 INFO @ Mon, 03 Jun 2019 03:06:50: 9000000 INFO @ Mon, 03 Jun 2019 03:06:53: 9000000 INFO @ Mon, 03 Jun 2019 03:06:57: 10000000 INFO @ Mon, 03 Jun 2019 03:06:58: 8000000 INFO @ Mon, 03 Jun 2019 03:07:01: 10000000 INFO @ Mon, 03 Jun 2019 03:07:04: 11000000 INFO @ Mon, 03 Jun 2019 03:07:07: 9000000 INFO @ Mon, 03 Jun 2019 03:07:09: 11000000 INFO @ Mon, 03 Jun 2019 03:07:11: 12000000 INFO @ Mon, 03 Jun 2019 03:07:16: 12000000 INFO @ Mon, 03 Jun 2019 03:07:17: 10000000 INFO @ Mon, 03 Jun 2019 03:07:18: 13000000 INFO @ Mon, 03 Jun 2019 03:07:21: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:07:21: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:07:21: #1 total tags in treatment: 13456228 INFO @ Mon, 03 Jun 2019 03:07:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:07:21: #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 03:07:21: #1 tags after filtering in treatment: 13456228 INFO @ Mon, 03 Jun 2019 03:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:07:21: #1 finished! INFO @ Mon, 03 Jun 2019 03:07:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:07:23: #2 number of paired peaks: 2657 INFO @ Mon, 03 Jun 2019 03:07:23: start model_add_line... INFO @ Mon, 03 Jun 2019 03:07:23: start X-correlation... INFO @ Mon, 03 Jun 2019 03:07:23: end of X-cor INFO @ Mon, 03 Jun 2019 03:07:23: #2 finished! INFO @ Mon, 03 Jun 2019 03:07:23: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 03:07:23: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 03:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.05_model.r INFO @ Mon, 03 Jun 2019 03:07:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:07:24: 13000000 INFO @ Mon, 03 Jun 2019 03:07:26: 11000000 INFO @ Mon, 03 Jun 2019 03:07:28: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:07:28: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:07:28: #1 total tags in treatment: 13456228 INFO @ Mon, 03 Jun 2019 03:07:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:07:28: #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 03:07:28: #1 tags after filtering in treatment: 13456228 INFO @ Mon, 03 Jun 2019 03:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:07:28: #1 finished! INFO @ Mon, 03 Jun 2019 03:07:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:07:30: #2 number of paired peaks: 2657 INFO @ Mon, 03 Jun 2019 03:07:30: start model_add_line... INFO @ Mon, 03 Jun 2019 03:07:30: start X-correlation... INFO @ Mon, 03 Jun 2019 03:07:30: end of X-cor INFO @ Mon, 03 Jun 2019 03:07:30: #2 finished! INFO @ Mon, 03 Jun 2019 03:07:30: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 03:07:30: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 03:07:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.20_model.r INFO @ Mon, 03 Jun 2019 03:07:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:07:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:07:35: 12000000 INFO @ Mon, 03 Jun 2019 03:07:44: 13000000 INFO @ Mon, 03 Jun 2019 03:07:48: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:07:48: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:07:48: #1 total tags in treatment: 13456228 INFO @ Mon, 03 Jun 2019 03:07:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:07:48: #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 03:07:48: #1 tags after filtering in treatment: 13456228 INFO @ Mon, 03 Jun 2019 03:07:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:07:48: #1 finished! INFO @ Mon, 03 Jun 2019 03:07:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:07:50: #2 number of paired peaks: 2657 INFO @ Mon, 03 Jun 2019 03:07:50: start model_add_line... INFO @ Mon, 03 Jun 2019 03:07:50: start X-correlation... INFO @ Mon, 03 Jun 2019 03:07:50: end of X-cor INFO @ Mon, 03 Jun 2019 03:07:50: #2 finished! INFO @ Mon, 03 Jun 2019 03:07:50: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 03:07:50: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 03:07:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.10_model.r INFO @ Mon, 03 Jun 2019 03:07:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:07:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:08:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:08:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.05_summits.bed INFO @ Mon, 03 Jun 2019 03:08:21: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (13916 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:08:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.20_summits.bed INFO @ Mon, 03 Jun 2019 03:08:28: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4050 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:08:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:08:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:08:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:08:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128300/SRX128300.10_summits.bed INFO @ Mon, 03 Jun 2019 03:08:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8242 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。