Job ID = 1307182 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:05:52 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' 2019-06-03T13:05:52 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/sos/sra-pub-run-2/SRR8433311/SRR8433311.1' 2019-06-03T13:05:52 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8433311' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T13:05:52 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T13:05:53 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' 2019-06-03T13:05:53 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/sos/sra-pub-run-2/SRR8433311/SRR8433311.1' 2019-06-03T13:05:53 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8433311' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T13:05:53 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T13:10:18 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 ) 2019-06-03T13:14:40 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 ) 2019-06-03T13:22:46 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 ) 2019-06-03T13:26:16 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 : 24,824,135 reads read : 49,648,270 reads written : 24,824,135 reads 0-length : 24,824,135 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: 00:08:12 24824135 reads; of these: 24824135 (100.00%) were unpaired; of these: 551555 (2.22%) aligned 0 times 22560811 (90.88%) aligned exactly 1 time 1711769 (6.90%) aligned >1 times 97.78% overall alignment rate Time searching: 00:08:12 Overall time: 00:08:12 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_rmdupse_core] 13181179 / 24272580 = 0.5430 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 22:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.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 22:44:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:44:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.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 22:44:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:44:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.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 22:44:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:44:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:45:02: 1000000 INFO @ Mon, 03 Jun 2019 22:45:02: 1000000 INFO @ Mon, 03 Jun 2019 22:45:05: 1000000 INFO @ Mon, 03 Jun 2019 22:45:10: 2000000 INFO @ Mon, 03 Jun 2019 22:45:12: 2000000 INFO @ Mon, 03 Jun 2019 22:45:17: 2000000 INFO @ Mon, 03 Jun 2019 22:45:18: 3000000 INFO @ Mon, 03 Jun 2019 22:45:20: 3000000 INFO @ Mon, 03 Jun 2019 22:45:27: 4000000 INFO @ Mon, 03 Jun 2019 22:45:28: 3000000 INFO @ Mon, 03 Jun 2019 22:45:30: 4000000 INFO @ Mon, 03 Jun 2019 22:45:37: 5000000 INFO @ Mon, 03 Jun 2019 22:45:39: 5000000 INFO @ Mon, 03 Jun 2019 22:45:40: 4000000 INFO @ Mon, 03 Jun 2019 22:45:45: 6000000 INFO @ Mon, 03 Jun 2019 22:45:48: 6000000 INFO @ Mon, 03 Jun 2019 22:45:51: 5000000 INFO @ Mon, 03 Jun 2019 22:45:55: 7000000 INFO @ Mon, 03 Jun 2019 22:45:57: 7000000 INFO @ Mon, 03 Jun 2019 22:46:02: 6000000 INFO @ Mon, 03 Jun 2019 22:46:03: 8000000 INFO @ Mon, 03 Jun 2019 22:46:06: 8000000 INFO @ Mon, 03 Jun 2019 22:46:11: 9000000 INFO @ Mon, 03 Jun 2019 22:46:13: 7000000 INFO @ Mon, 03 Jun 2019 22:46:14: 9000000 INFO @ Mon, 03 Jun 2019 22:46:20: 10000000 INFO @ Mon, 03 Jun 2019 22:46:23: 10000000 INFO @ Mon, 03 Jun 2019 22:46:24: 8000000 INFO @ Mon, 03 Jun 2019 22:46:28: 11000000 INFO @ Mon, 03 Jun 2019 22:46:29: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:46:29: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:46:29: #1 total tags in treatment: 11091401 INFO @ Mon, 03 Jun 2019 22:46:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:46:29: #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 22:46:29: #1 tags after filtering in treatment: 11091401 INFO @ Mon, 03 Jun 2019 22:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:46:29: #1 finished! INFO @ Mon, 03 Jun 2019 22:46:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:46:31: #2 number of paired peaks: 13798 INFO @ Mon, 03 Jun 2019 22:46:31: start model_add_line... INFO @ Mon, 03 Jun 2019 22:46:32: start X-correlation... INFO @ Mon, 03 Jun 2019 22:46:32: end of X-cor INFO @ Mon, 03 Jun 2019 22:46:32: #2 finished! INFO @ Mon, 03 Jun 2019 22:46:32: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 22:46:32: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 22:46:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.05_model.r WARNING @ Mon, 03 Jun 2019 22:46:32: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:46:32: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Mon, 03 Jun 2019 22:46:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:46:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:46:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:46:32: 11000000 INFO @ Mon, 03 Jun 2019 22:46:33: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:46:33: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:46:33: #1 total tags in treatment: 11091401 INFO @ Mon, 03 Jun 2019 22:46:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:46:33: #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 22:46:33: #1 tags after filtering in treatment: 11091401 INFO @ Mon, 03 Jun 2019 22:46:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:46:33: #1 finished! INFO @ Mon, 03 Jun 2019 22:46:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:46:35: 9000000 INFO @ Mon, 03 Jun 2019 22:46:36: #2 number of paired peaks: 13798 INFO @ Mon, 03 Jun 2019 22:46:36: start model_add_line... INFO @ Mon, 03 Jun 2019 22:46:36: start X-correlation... INFO @ Mon, 03 Jun 2019 22:46:36: end of X-cor INFO @ Mon, 03 Jun 2019 22:46:36: #2 finished! INFO @ Mon, 03 Jun 2019 22:46:36: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 22:46:36: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 22:46:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.10_model.r WARNING @ Mon, 03 Jun 2019 22:46:36: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:46:36: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Mon, 03 Jun 2019 22:46:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:46:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:46:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:46:46: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 22:46:56: 11000000 INFO @ Mon, 03 Jun 2019 22:46:57: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:46:57: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:46:57: #1 total tags in treatment: 11091401 INFO @ Mon, 03 Jun 2019 22:46:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:46:57: #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 22:46:57: #1 tags after filtering in treatment: 11091401 INFO @ Mon, 03 Jun 2019 22:46:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:46:57: #1 finished! INFO @ Mon, 03 Jun 2019 22:46:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:46:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:47:00: #2 number of paired peaks: 13798 INFO @ Mon, 03 Jun 2019 22:47:00: start model_add_line... INFO @ Mon, 03 Jun 2019 22:47:00: start X-correlation... INFO @ Mon, 03 Jun 2019 22:47:00: end of X-cor INFO @ Mon, 03 Jun 2019 22:47:00: #2 finished! INFO @ Mon, 03 Jun 2019 22:47:00: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 22:47:00: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 22:47:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.20_model.r WARNING @ Mon, 03 Jun 2019 22:47:00: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:47:00: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Mon, 03 Jun 2019 22:47:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:47:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:47:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 22:47:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:47:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:47:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:47:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:47:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.05_summits.bed INFO @ Mon, 03 Jun 2019 22:47:19: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9630 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:47:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:47:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:47:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.10_summits.bed INFO @ Mon, 03 Jun 2019 22:47:23: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8973 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:47:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241030/SRX5241030.20_summits.bed INFO @ Mon, 03 Jun 2019 22:47:46: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8057 records, 4 fields): 12 millis CompletedMACS2peakCalling