Job ID = 1294321 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T21:19:51 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 ) 2019-06-02T21:19:51 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 ) 2019-06-02T21:19:51 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 ) 2019-06-02T21:19:51 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 ) 2019-06-02T21:27:43 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 ) 2019-06-02T21:28:30 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T21:28:30 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 14,890,953 reads read : 29,781,906 reads written : 29,781,906 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: 00:39:13 14890953 reads; of these: 14890953 (100.00%) were paired; of these: 1132636 (7.61%) aligned concordantly 0 times 10136463 (68.07%) aligned concordantly exactly 1 time 3621854 (24.32%) aligned concordantly >1 times ---- 1132636 pairs aligned concordantly 0 times; of these: 121110 (10.69%) aligned discordantly 1 time ---- 1011526 pairs aligned 0 times concordantly or discordantly; of these: 2023052 mates make up the pairs; of these: 969723 (47.93%) aligned 0 times 607626 (30.04%) aligned exactly 1 time 445703 (22.03%) aligned >1 times 96.74% overall alignment rate Time searching: 00:39:13 Overall time: 00:39:13 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_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] 7815440 / 13827394 = 0.5652 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 07:20:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.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 07:20:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:20:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:20:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.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 07:20:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:20:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:20:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.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 07:20:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:20:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:20:37: 1000000 INFO @ Mon, 03 Jun 2019 07:20:37: 1000000 INFO @ Mon, 03 Jun 2019 07:20:38: 1000000 INFO @ Mon, 03 Jun 2019 07:20:48: 2000000 INFO @ Mon, 03 Jun 2019 07:20:49: 2000000 INFO @ Mon, 03 Jun 2019 07:20:50: 2000000 INFO @ Mon, 03 Jun 2019 07:20:58: 3000000 INFO @ Mon, 03 Jun 2019 07:21:01: 3000000 INFO @ Mon, 03 Jun 2019 07:21:01: 3000000 INFO @ Mon, 03 Jun 2019 07:21:08: 4000000 INFO @ Mon, 03 Jun 2019 07:21:13: 4000000 INFO @ Mon, 03 Jun 2019 07:21:13: 4000000 INFO @ Mon, 03 Jun 2019 07:21:18: 5000000 INFO @ Mon, 03 Jun 2019 07:21:24: 5000000 INFO @ Mon, 03 Jun 2019 07:21:25: 5000000 INFO @ Mon, 03 Jun 2019 07:21:28: 6000000 INFO @ Mon, 03 Jun 2019 07:21:36: 6000000 INFO @ Mon, 03 Jun 2019 07:21:36: 6000000 INFO @ Mon, 03 Jun 2019 07:21:38: 7000000 INFO @ Mon, 03 Jun 2019 07:21:47: 7000000 INFO @ Mon, 03 Jun 2019 07:21:47: 7000000 INFO @ Mon, 03 Jun 2019 07:21:48: 8000000 INFO @ Mon, 03 Jun 2019 07:21:57: 9000000 INFO @ Mon, 03 Jun 2019 07:21:58: 8000000 INFO @ Mon, 03 Jun 2019 07:21:59: 8000000 INFO @ Mon, 03 Jun 2019 07:22:07: 10000000 INFO @ Mon, 03 Jun 2019 07:22:09: 9000000 INFO @ Mon, 03 Jun 2019 07:22:10: 9000000 INFO @ Mon, 03 Jun 2019 07:22:17: 11000000 INFO @ Mon, 03 Jun 2019 07:22:20: 10000000 INFO @ Mon, 03 Jun 2019 07:22:21: 10000000 INFO @ Mon, 03 Jun 2019 07:22:27: 12000000 INFO @ Mon, 03 Jun 2019 07:22:31: 11000000 INFO @ Mon, 03 Jun 2019 07:22:32: 11000000 INFO @ Mon, 03 Jun 2019 07:22:37: 13000000 INFO @ Mon, 03 Jun 2019 07:22:39: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 07:22:39: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 07:22:39: #1 total tags in treatment: 5979016 INFO @ Mon, 03 Jun 2019 07:22:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:22:39: #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 07:22:39: #1 tags after filtering in treatment: 5248885 INFO @ Mon, 03 Jun 2019 07:22:39: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 07:22:39: #1 finished! INFO @ Mon, 03 Jun 2019 07:22:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:22:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:22:40: #2 number of paired peaks: 4042 INFO @ Mon, 03 Jun 2019 07:22:40: start model_add_line... INFO @ Mon, 03 Jun 2019 07:22:40: start X-correlation... INFO @ Mon, 03 Jun 2019 07:22:40: end of X-cor INFO @ Mon, 03 Jun 2019 07:22:40: #2 finished! INFO @ Mon, 03 Jun 2019 07:22:40: #2 predicted fragment length is 224 bps INFO @ Mon, 03 Jun 2019 07:22:40: #2 alternative fragment length(s) may be 224 bps INFO @ Mon, 03 Jun 2019 07:22:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.05_model.r INFO @ Mon, 03 Jun 2019 07:22:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:22:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:22:42: 12000000 INFO @ Mon, 03 Jun 2019 07:22:43: 12000000 INFO @ Mon, 03 Jun 2019 07:22:53: 13000000 INFO @ Mon, 03 Jun 2019 07:22:54: 13000000 INFO @ Mon, 03 Jun 2019 07:22:55: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 07:22:55: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 07:22:55: #1 total tags in treatment: 5979016 INFO @ Mon, 03 Jun 2019 07:22:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:22:55: #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 07:22:55: #1 tags after filtering in treatment: 5248885 INFO @ Mon, 03 Jun 2019 07:22:55: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 07:22:55: #1 finished! INFO @ Mon, 03 Jun 2019 07:22:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:22:55: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 07:22:55: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 07:22:55: #1 total tags in treatment: 5979016 INFO @ Mon, 03 Jun 2019 07:22:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:22:55: #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 07:22:55: #1 tags after filtering in treatment: 5248885 INFO @ Mon, 03 Jun 2019 07:22:55: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 07:22:55: #1 finished! INFO @ Mon, 03 Jun 2019 07:22:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:22:56: #2 number of paired peaks: 4042 INFO @ Mon, 03 Jun 2019 07:22:56: start model_add_line... INFO @ Mon, 03 Jun 2019 07:22:56: start X-correlation... INFO @ Mon, 03 Jun 2019 07:22:56: end of X-cor INFO @ Mon, 03 Jun 2019 07:22:56: #2 finished! INFO @ Mon, 03 Jun 2019 07:22:56: #2 predicted fragment length is 224 bps INFO @ Mon, 03 Jun 2019 07:22:56: #2 alternative fragment length(s) may be 224 bps INFO @ Mon, 03 Jun 2019 07:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.20_model.r INFO @ Mon, 03 Jun 2019 07:22:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:22:56: #2 number of paired peaks: 4042 INFO @ Mon, 03 Jun 2019 07:22:56: start model_add_line... INFO @ Mon, 03 Jun 2019 07:22:56: start X-correlation... INFO @ Mon, 03 Jun 2019 07:22:56: end of X-cor INFO @ Mon, 03 Jun 2019 07:22:56: #2 finished! INFO @ Mon, 03 Jun 2019 07:22:56: #2 predicted fragment length is 224 bps INFO @ Mon, 03 Jun 2019 07:22:56: #2 alternative fragment length(s) may be 224 bps INFO @ Mon, 03 Jun 2019 07:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.10_model.r INFO @ Mon, 03 Jun 2019 07:22:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:23:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:23:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:23:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:23:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.05_summits.bed INFO @ Mon, 03 Jun 2019 07:23:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4359 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:23:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:23:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:23:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:23:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:23:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.20_summits.bed INFO @ Mon, 03 Jun 2019 07:23:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1478 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:23:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:23:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:23:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2432254/SRX2432254.10_summits.bed INFO @ Mon, 03 Jun 2019 07:23:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2600 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。