Job ID = 1293839 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T17:41:14 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T17:41:14 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra3/SRR/000431/SRR442320' 2019-06-02T17:41:23 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR442320', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T17:42:48 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 ) 2019-06-02T17:43:27 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 ) 2019-06-02T17:54:54 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 : 28,528,210 reads read : 57,056,420 reads written : 57,056,420 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: 00:44:05 28528210 reads; of these: 28528210 (100.00%) were paired; of these: 9690993 (33.97%) aligned concordantly 0 times 14405802 (50.50%) aligned concordantly exactly 1 time 4431415 (15.53%) aligned concordantly >1 times ---- 9690993 pairs aligned concordantly 0 times; of these: 129294 (1.33%) aligned discordantly 1 time ---- 9561699 pairs aligned 0 times concordantly or discordantly; of these: 19123398 mates make up the pairs; of these: 18555253 (97.03%) aligned 0 times 396468 (2.07%) aligned exactly 1 time 171677 (0.90%) aligned >1 times 67.48% overall alignment rate Time searching: 00:44:05 Overall time: 00:44:05 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 16 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] 11573533 / 18927052 = 0.6115 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 04:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.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 04:08:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:08:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.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 04:08:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:08:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:08:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.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 04:08:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:08:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:08:10: 1000000 INFO @ Mon, 03 Jun 2019 04:08:11: 1000000 INFO @ Mon, 03 Jun 2019 04:08:12: 1000000 INFO @ Mon, 03 Jun 2019 04:08:16: 2000000 INFO @ Mon, 03 Jun 2019 04:08:18: 2000000 INFO @ Mon, 03 Jun 2019 04:08:20: 2000000 INFO @ Mon, 03 Jun 2019 04:08:22: 3000000 INFO @ Mon, 03 Jun 2019 04:08:25: 3000000 INFO @ Mon, 03 Jun 2019 04:08:28: 3000000 INFO @ Mon, 03 Jun 2019 04:08:29: 4000000 INFO @ Mon, 03 Jun 2019 04:08:32: 4000000 INFO @ Mon, 03 Jun 2019 04:08:35: 5000000 INFO @ Mon, 03 Jun 2019 04:08:36: 4000000 INFO @ Mon, 03 Jun 2019 04:08:38: 5000000 INFO @ Mon, 03 Jun 2019 04:08:41: 6000000 INFO @ Mon, 03 Jun 2019 04:08:44: 5000000 INFO @ Mon, 03 Jun 2019 04:08:45: 6000000 INFO @ Mon, 03 Jun 2019 04:08:47: 7000000 INFO @ Mon, 03 Jun 2019 04:08:51: 7000000 INFO @ Mon, 03 Jun 2019 04:08:52: 6000000 INFO @ Mon, 03 Jun 2019 04:08:53: 8000000 INFO @ Mon, 03 Jun 2019 04:08:58: 8000000 INFO @ Mon, 03 Jun 2019 04:09:00: 7000000 INFO @ Mon, 03 Jun 2019 04:09:00: 9000000 INFO @ Mon, 03 Jun 2019 04:09:05: 9000000 INFO @ Mon, 03 Jun 2019 04:09:06: 10000000 INFO @ Mon, 03 Jun 2019 04:09:07: 8000000 INFO @ Mon, 03 Jun 2019 04:09:12: 10000000 INFO @ Mon, 03 Jun 2019 04:09:12: 11000000 INFO @ Mon, 03 Jun 2019 04:09:15: 9000000 INFO @ Mon, 03 Jun 2019 04:09:18: 12000000 INFO @ Mon, 03 Jun 2019 04:09:19: 11000000 INFO @ Mon, 03 Jun 2019 04:09:23: 10000000 INFO @ Mon, 03 Jun 2019 04:09:24: 13000000 INFO @ Mon, 03 Jun 2019 04:09:26: 12000000 INFO @ Mon, 03 Jun 2019 04:09:30: 14000000 INFO @ Mon, 03 Jun 2019 04:09:31: 11000000 INFO @ Mon, 03 Jun 2019 04:09:32: 13000000 INFO @ Mon, 03 Jun 2019 04:09:36: 15000000 INFO @ Mon, 03 Jun 2019 04:09:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:09:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:09:39: #1 total tags in treatment: 7305817 INFO @ Mon, 03 Jun 2019 04:09:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:09:39: #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 04:09:39: #1 tags after filtering in treatment: 6507564 INFO @ Mon, 03 Jun 2019 04:09:39: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 04:09:39: #1 finished! INFO @ Mon, 03 Jun 2019 04:09:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:09:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:09:39: 14000000 INFO @ Mon, 03 Jun 2019 04:09:39: 12000000 INFO @ Mon, 03 Jun 2019 04:09:40: #2 number of paired peaks: 2711 INFO @ Mon, 03 Jun 2019 04:09:40: start model_add_line... INFO @ Mon, 03 Jun 2019 04:09:40: start X-correlation... INFO @ Mon, 03 Jun 2019 04:09:40: end of X-cor INFO @ Mon, 03 Jun 2019 04:09:40: #2 finished! INFO @ Mon, 03 Jun 2019 04:09:40: #2 predicted fragment length is 107 bps INFO @ Mon, 03 Jun 2019 04:09:40: #2 alternative fragment length(s) may be 107 bps INFO @ Mon, 03 Jun 2019 04:09:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.20_model.r INFO @ Mon, 03 Jun 2019 04:09:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:09:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:09:46: 15000000 INFO @ Mon, 03 Jun 2019 04:09:47: 13000000 INFO @ Mon, 03 Jun 2019 04:09:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:09:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:09:48: #1 total tags in treatment: 7305817 INFO @ Mon, 03 Jun 2019 04:09:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:09:48: #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 04:09:48: #1 tags after filtering in treatment: 6507564 INFO @ Mon, 03 Jun 2019 04:09:48: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 04:09:48: #1 finished! INFO @ Mon, 03 Jun 2019 04:09:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:09:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:09:49: #2 number of paired peaks: 2711 INFO @ Mon, 03 Jun 2019 04:09:49: start model_add_line... INFO @ Mon, 03 Jun 2019 04:09:49: start X-correlation... INFO @ Mon, 03 Jun 2019 04:09:49: end of X-cor INFO @ Mon, 03 Jun 2019 04:09:49: #2 finished! INFO @ Mon, 03 Jun 2019 04:09:49: #2 predicted fragment length is 107 bps INFO @ Mon, 03 Jun 2019 04:09:49: #2 alternative fragment length(s) may be 107 bps INFO @ Mon, 03 Jun 2019 04:09:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.10_model.r INFO @ Mon, 03 Jun 2019 04:09:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:09:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:09:55: 14000000 INFO @ Mon, 03 Jun 2019 04:10:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:10:02: 15000000 INFO @ Mon, 03 Jun 2019 04:10:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:10:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:10:05: #1 total tags in treatment: 7305817 INFO @ Mon, 03 Jun 2019 04:10:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:10:05: #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 04:10:05: #1 tags after filtering in treatment: 6507564 INFO @ Mon, 03 Jun 2019 04:10:05: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 04:10:05: #1 finished! INFO @ Mon, 03 Jun 2019 04:10:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:10:06: #2 number of paired peaks: 2711 INFO @ Mon, 03 Jun 2019 04:10:06: start model_add_line... INFO @ Mon, 03 Jun 2019 04:10:06: start X-correlation... INFO @ Mon, 03 Jun 2019 04:10:06: end of X-cor INFO @ Mon, 03 Jun 2019 04:10:06: #2 finished! INFO @ Mon, 03 Jun 2019 04:10:06: #2 predicted fragment length is 107 bps INFO @ Mon, 03 Jun 2019 04:10:06: #2 alternative fragment length(s) may be 107 bps INFO @ Mon, 03 Jun 2019 04:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.05_model.r INFO @ Mon, 03 Jun 2019 04:10:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:10:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:10:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:10:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:10:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.20_summits.bed INFO @ Mon, 03 Jun 2019 04:10:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2208 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:10:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:10:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:10:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.10_summits.bed INFO @ Mon, 03 Jun 2019 04:10:19: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3999 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:10:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128325/SRX128325.05_summits.bed INFO @ Mon, 03 Jun 2019 04:10:36: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7401 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。