Job ID = 1294041 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T19:23:57 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 : 4,359,021 reads read : 8,718,042 reads written : 8,718,042 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: 00:10:04 4359021 reads; of these: 4359021 (100.00%) were paired; of these: 644148 (14.78%) aligned concordantly 0 times 3114095 (71.44%) aligned concordantly exactly 1 time 600778 (13.78%) aligned concordantly >1 times ---- 644148 pairs aligned concordantly 0 times; of these: 280633 (43.57%) aligned discordantly 1 time ---- 363515 pairs aligned 0 times concordantly or discordantly; of these: 727030 mates make up the pairs; of these: 466134 (64.11%) aligned 0 times 117850 (16.21%) aligned exactly 1 time 143046 (19.68%) aligned >1 times 94.65% overall alignment rate Time searching: 00:10:04 Overall time: 00:10:04 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 115236 / 3991810 = 0.0289 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 04:38:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.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 04:38:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:38:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:38:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.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 04:38:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:38:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:38:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.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 04:38:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:38:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:39:00: 1000000 INFO @ Mon, 03 Jun 2019 04:39:02: 1000000 INFO @ Mon, 03 Jun 2019 04:39:02: 1000000 INFO @ Mon, 03 Jun 2019 04:39:09: 2000000 INFO @ Mon, 03 Jun 2019 04:39:12: 2000000 INFO @ Mon, 03 Jun 2019 04:39:12: 2000000 INFO @ Mon, 03 Jun 2019 04:39:17: 3000000 INFO @ Mon, 03 Jun 2019 04:39:22: 3000000 INFO @ Mon, 03 Jun 2019 04:39:23: 3000000 INFO @ Mon, 03 Jun 2019 04:39:26: 4000000 INFO @ Mon, 03 Jun 2019 04:39:32: 4000000 INFO @ Mon, 03 Jun 2019 04:39:33: 4000000 INFO @ Mon, 03 Jun 2019 04:39:34: 5000000 INFO @ Mon, 03 Jun 2019 04:39:41: 5000000 INFO @ Mon, 03 Jun 2019 04:39:43: 5000000 INFO @ Mon, 03 Jun 2019 04:39:43: 6000000 INFO @ Mon, 03 Jun 2019 04:39:51: 6000000 INFO @ Mon, 03 Jun 2019 04:39:52: 7000000 INFO @ Mon, 03 Jun 2019 04:39:53: 6000000 INFO @ Mon, 03 Jun 2019 04:40:00: 8000000 INFO @ Mon, 03 Jun 2019 04:40:00: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:40:00: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:40:00: #1 total tags in treatment: 3602887 INFO @ Mon, 03 Jun 2019 04:40:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:40:00: #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 04:40:00: #1 tags after filtering in treatment: 3431670 INFO @ Mon, 03 Jun 2019 04:40:00: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:40:00: #1 finished! INFO @ Mon, 03 Jun 2019 04:40:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:40:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:40:01: #2 number of paired peaks: 3313 INFO @ Mon, 03 Jun 2019 04:40:01: start model_add_line... INFO @ Mon, 03 Jun 2019 04:40:01: start X-correlation... INFO @ Mon, 03 Jun 2019 04:40:01: end of X-cor INFO @ Mon, 03 Jun 2019 04:40:01: #2 finished! INFO @ Mon, 03 Jun 2019 04:40:01: #2 predicted fragment length is 214 bps INFO @ Mon, 03 Jun 2019 04:40:01: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 03 Jun 2019 04:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.10_model.r INFO @ Mon, 03 Jun 2019 04:40:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:40:02: 7000000 INFO @ Mon, 03 Jun 2019 04:40:04: 7000000 INFO @ Mon, 03 Jun 2019 04:40:12: 8000000 INFO @ Mon, 03 Jun 2019 04:40:12: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:40:12: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:40:12: #1 total tags in treatment: 3602887 INFO @ Mon, 03 Jun 2019 04:40:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:40:12: #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 04:40:12: #1 tags after filtering in treatment: 3431670 INFO @ Mon, 03 Jun 2019 04:40:12: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:40:12: #1 finished! INFO @ Mon, 03 Jun 2019 04:40:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:40:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:40:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:40:13: #2 number of paired peaks: 3313 INFO @ Mon, 03 Jun 2019 04:40:13: start model_add_line... INFO @ Mon, 03 Jun 2019 04:40:13: start X-correlation... INFO @ Mon, 03 Jun 2019 04:40:13: end of X-cor INFO @ Mon, 03 Jun 2019 04:40:13: #2 finished! INFO @ Mon, 03 Jun 2019 04:40:13: #2 predicted fragment length is 214 bps INFO @ Mon, 03 Jun 2019 04:40:13: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 03 Jun 2019 04:40:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.20_model.r INFO @ Mon, 03 Jun 2019 04:40:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:40:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:40:14: 8000000 INFO @ Mon, 03 Jun 2019 04:40:14: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:40:14: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:40:14: #1 total tags in treatment: 3602887 INFO @ Mon, 03 Jun 2019 04:40:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:40:14: #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 04:40:14: #1 tags after filtering in treatment: 3431670 INFO @ Mon, 03 Jun 2019 04:40:14: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:40:14: #1 finished! INFO @ Mon, 03 Jun 2019 04:40:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:40:15: #2 number of paired peaks: 3313 INFO @ Mon, 03 Jun 2019 04:40:15: start model_add_line... INFO @ Mon, 03 Jun 2019 04:40:15: start X-correlation... INFO @ Mon, 03 Jun 2019 04:40:15: end of X-cor INFO @ Mon, 03 Jun 2019 04:40:15: #2 finished! INFO @ Mon, 03 Jun 2019 04:40:15: #2 predicted fragment length is 214 bps INFO @ Mon, 03 Jun 2019 04:40:15: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 03 Jun 2019 04:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.05_model.r INFO @ Mon, 03 Jun 2019 04:40:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:40:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:40:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:40:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.10_summits.bed INFO @ Mon, 03 Jun 2019 04:40:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3743 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:40:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:40:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:40:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:40:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:40:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.20_summits.bed INFO @ Mon, 03 Jun 2019 04:40:30: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2280 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:40:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763407/SRX1763407.05_summits.bed INFO @ Mon, 03 Jun 2019 04:40:33: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5225 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。