Job ID = 4178494 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:25:38 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-12-05T03:25:38 fasterq-dump.2.9.6 int: file not open while identifying file within network system module - cannot KSocketGetRemoteEndpoint 2019-12-05T03:25:38 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing unknown IP from '172.19.7.131' 2019-12-05T03:25:38 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'www.ncbi.nlm.nih.gov' (130.14.29.110) from '172.19.7.131' 2019-12-05T03:25:48 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR8743321', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 16,449,917 reads read : 16,449,917 reads written : 16,449,917 rm: cannot remove ‘[DSE]RR*’: 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: 00:05:42 16449917 reads; of these: 16449917 (100.00%) were unpaired; of these: 532719 (3.24%) aligned 0 times 11300458 (68.70%) aligned exactly 1 time 4616740 (28.07%) aligned >1 times 96.76% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 3985195 / 15917198 = 0.2504 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:42:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.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 @ Thu, 05 Dec 2019 12:42:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:42:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:43:04: 1000000 INFO @ Thu, 05 Dec 2019 12:43:10: 2000000 INFO @ Thu, 05 Dec 2019 12:43:16: 3000000 INFO @ Thu, 05 Dec 2019 12:43:22: 4000000 INFO @ Thu, 05 Dec 2019 12:43:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.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 @ Thu, 05 Dec 2019 12:43:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:43:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:43:28: 5000000 INFO @ Thu, 05 Dec 2019 12:43:33: 1000000 INFO @ Thu, 05 Dec 2019 12:43:34: 6000000 INFO @ Thu, 05 Dec 2019 12:43:39: 2000000 INFO @ Thu, 05 Dec 2019 12:43:40: 7000000 INFO @ Thu, 05 Dec 2019 12:43:44: 3000000 INFO @ Thu, 05 Dec 2019 12:43:46: 8000000 INFO @ Thu, 05 Dec 2019 12:43:49: 4000000 INFO @ Thu, 05 Dec 2019 12:43:52: 9000000 INFO @ Thu, 05 Dec 2019 12:43:55: 5000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:43:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.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 @ Thu, 05 Dec 2019 12:43:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:43:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:43:59: 10000000 INFO @ Thu, 05 Dec 2019 12:44:00: 6000000 INFO @ Thu, 05 Dec 2019 12:44:04: 1000000 INFO @ Thu, 05 Dec 2019 12:44:05: 11000000 INFO @ Thu, 05 Dec 2019 12:44:06: 7000000 INFO @ Thu, 05 Dec 2019 12:44:10: 2000000 INFO @ Thu, 05 Dec 2019 12:44:10: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:44:10: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:44:10: #1 total tags in treatment: 11932003 INFO @ Thu, 05 Dec 2019 12:44:10: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:44:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:44:11: #1 tags after filtering in treatment: 11932003 INFO @ Thu, 05 Dec 2019 12:44:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:44:11: #1 finished! INFO @ Thu, 05 Dec 2019 12:44:11: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:44:11: #2 number of paired peaks: 1133 INFO @ Thu, 05 Dec 2019 12:44:11: start model_add_line... INFO @ Thu, 05 Dec 2019 12:44:12: start X-correlation... INFO @ Thu, 05 Dec 2019 12:44:12: end of X-cor INFO @ Thu, 05 Dec 2019 12:44:12: #2 finished! INFO @ Thu, 05 Dec 2019 12:44:12: #2 predicted fragment length is 143 bps INFO @ Thu, 05 Dec 2019 12:44:12: #2 alternative fragment length(s) may be 16,143,252,457,583 bps INFO @ Thu, 05 Dec 2019 12:44:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.05_model.r INFO @ Thu, 05 Dec 2019 12:44:12: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:44:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:44:12: 8000000 INFO @ Thu, 05 Dec 2019 12:44:16: 3000000 INFO @ Thu, 05 Dec 2019 12:44:18: 9000000 INFO @ Thu, 05 Dec 2019 12:44:22: 4000000 INFO @ Thu, 05 Dec 2019 12:44:24: 10000000 INFO @ Thu, 05 Dec 2019 12:44:27: 5000000 INFO @ Thu, 05 Dec 2019 12:44:29: 11000000 INFO @ Thu, 05 Dec 2019 12:44:33: 6000000 INFO @ Thu, 05 Dec 2019 12:44:35: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:44:35: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:44:35: #1 total tags in treatment: 11932003 INFO @ Thu, 05 Dec 2019 12:44:35: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:44:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:44:35: #1 tags after filtering in treatment: 11932003 INFO @ Thu, 05 Dec 2019 12:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:44:35: #1 finished! INFO @ Thu, 05 Dec 2019 12:44:35: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:44:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:44:35: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:44:36: #2 number of paired peaks: 1133 INFO @ Thu, 05 Dec 2019 12:44:36: start model_add_line... INFO @ Thu, 05 Dec 2019 12:44:36: start X-correlation... INFO @ Thu, 05 Dec 2019 12:44:36: end of X-cor INFO @ Thu, 05 Dec 2019 12:44:36: #2 finished! INFO @ Thu, 05 Dec 2019 12:44:36: #2 predicted fragment length is 143 bps INFO @ Thu, 05 Dec 2019 12:44:36: #2 alternative fragment length(s) may be 16,143,252,457,583 bps INFO @ Thu, 05 Dec 2019 12:44:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.10_model.r INFO @ Thu, 05 Dec 2019 12:44:36: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:44:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:44:39: 7000000 INFO @ Thu, 05 Dec 2019 12:44:44: 8000000 INFO @ Thu, 05 Dec 2019 12:44:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:44:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:44:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.05_summits.bed INFO @ Thu, 05 Dec 2019 12:44:48: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2285 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:44:49: 9000000 INFO @ Thu, 05 Dec 2019 12:44:55: 10000000 INFO @ Thu, 05 Dec 2019 12:44:59: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:45:00: 11000000 INFO @ Thu, 05 Dec 2019 12:45:05: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:45:05: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:45:05: #1 total tags in treatment: 11932003 INFO @ Thu, 05 Dec 2019 12:45:05: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:45:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:45:06: #1 tags after filtering in treatment: 11932003 INFO @ Thu, 05 Dec 2019 12:45:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:45:06: #1 finished! INFO @ Thu, 05 Dec 2019 12:45:06: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:45:06: #2 number of paired peaks: 1133 INFO @ Thu, 05 Dec 2019 12:45:06: start model_add_line... INFO @ Thu, 05 Dec 2019 12:45:07: start X-correlation... INFO @ Thu, 05 Dec 2019 12:45:07: end of X-cor INFO @ Thu, 05 Dec 2019 12:45:07: #2 finished! INFO @ Thu, 05 Dec 2019 12:45:07: #2 predicted fragment length is 143 bps INFO @ Thu, 05 Dec 2019 12:45:07: #2 alternative fragment length(s) may be 16,143,252,457,583 bps INFO @ Thu, 05 Dec 2019 12:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.20_model.r INFO @ Thu, 05 Dec 2019 12:45:07: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:45:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:45:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:45:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.10_summits.bed INFO @ Thu, 05 Dec 2019 12:45:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1146 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:45:30: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535393/SRX5535393.20_summits.bed INFO @ Thu, 05 Dec 2019 12:45:43: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。