Job ID = 3785921 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:36:47 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 ) 2019-11-01T05:36:47 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.70' 2019-11-01T05:36:47 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.25) from '172.19.7.70' 2019-11-01T05:36:47 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra71/SRR/009381/SRR9606651' 2019-11-01T05:36:47 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR9606651' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-11-01T05:36:47 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-11-01T05:38:29 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:39:20 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 ) 2019-11-01T05:39:31 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 ) 2019-11-01T05:39:49 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 ) 2019-11-01T05:40:06 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 ) 2019-11-01T05:40:42 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 ) 2019-11-01T05:41:17 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 ) 2019-11-01T05:44:31 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 ) 2019-11-01T05:45:05 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 ) 2019-11-01T05:45:05 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.70' 2019-11-01T05:45:05 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.27) from '172.19.7.70' 2019-11-01T05:46:33 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 ) 2019-11-01T05:49:32 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 ) 2019-11-01T05:52:33 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 ) 2019-11-01T05:53:14 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 : 10,009,728 reads read : 20,019,456 reads written : 10,009,728 reads 0-length : 10,009,728 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: 00:01:47 10009728 reads; of these: 10009728 (100.00%) were unpaired; of these: 9569663 (95.60%) aligned 0 times 304490 (3.04%) aligned exactly 1 time 135575 (1.35%) aligned >1 times 4.40% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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_rmdupse_core] 17954 / 440065 = 0.0408 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 14:57:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.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 @ Fri, 01 Nov 2019 14:57:45: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:57:45: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:57:49: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:57:49: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:57:49: #1 total tags in treatment: 422111 INFO @ Fri, 01 Nov 2019 14:57:49: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:57:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:57:49: #1 tags after filtering in treatment: 422110 INFO @ Fri, 01 Nov 2019 14:57:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:57:49: #1 finished! INFO @ Fri, 01 Nov 2019 14:57:49: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:57:49: #2 number of paired peaks: 1260 INFO @ Fri, 01 Nov 2019 14:57:49: start model_add_line... INFO @ Fri, 01 Nov 2019 14:57:49: start X-correlation... INFO @ Fri, 01 Nov 2019 14:57:49: end of X-cor INFO @ Fri, 01 Nov 2019 14:57:49: #2 finished! INFO @ Fri, 01 Nov 2019 14:57:49: #2 predicted fragment length is 74 bps INFO @ Fri, 01 Nov 2019 14:57:49: #2 alternative fragment length(s) may be 74,216 bps INFO @ Fri, 01 Nov 2019 14:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.05_model.r WARNING @ Fri, 01 Nov 2019 14:57:49: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 14:57:49: #2 You may need to consider one of the other alternative d(s): 74,216 WARNING @ Fri, 01 Nov 2019 14:57:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 01 Nov 2019 14:57:49: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:57:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:57:50: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:57:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.05_peaks.xls INFO @ Fri, 01 Nov 2019 14:57:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:57:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.05_summits.bed INFO @ Fri, 01 Nov 2019 14:57:51: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:58:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.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 @ Fri, 01 Nov 2019 14:58:15: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:58:15: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:58:19: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:58:19: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:58:19: #1 total tags in treatment: 422111 INFO @ Fri, 01 Nov 2019 14:58:19: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:58:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:58:19: #1 tags after filtering in treatment: 422110 INFO @ Fri, 01 Nov 2019 14:58:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:58:19: #1 finished! INFO @ Fri, 01 Nov 2019 14:58:19: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:58:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:58:19: #2 number of paired peaks: 1260 INFO @ Fri, 01 Nov 2019 14:58:19: start model_add_line... INFO @ Fri, 01 Nov 2019 14:58:19: start X-correlation... INFO @ Fri, 01 Nov 2019 14:58:19: end of X-cor INFO @ Fri, 01 Nov 2019 14:58:19: #2 finished! INFO @ Fri, 01 Nov 2019 14:58:19: #2 predicted fragment length is 74 bps INFO @ Fri, 01 Nov 2019 14:58:19: #2 alternative fragment length(s) may be 74,216 bps INFO @ Fri, 01 Nov 2019 14:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.10_model.r WARNING @ Fri, 01 Nov 2019 14:58:19: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 14:58:19: #2 You may need to consider one of the other alternative d(s): 74,216 WARNING @ Fri, 01 Nov 2019 14:58:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 01 Nov 2019 14:58:19: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:58:20: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:58:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.10_peaks.xls INFO @ Fri, 01 Nov 2019 14:58:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:58:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.10_summits.bed INFO @ Fri, 01 Nov 2019 14:58:21: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Fri, 01 Nov 2019 14:58:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.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 @ Fri, 01 Nov 2019 14:58:45: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:58:45: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:58:49: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:58:49: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:58:49: #1 total tags in treatment: 422111 INFO @ Fri, 01 Nov 2019 14:58:49: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:58:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:58:49: #1 tags after filtering in treatment: 422110 INFO @ Fri, 01 Nov 2019 14:58:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:58:49: #1 finished! INFO @ Fri, 01 Nov 2019 14:58:49: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:58:49: #2 number of paired peaks: 1260 INFO @ Fri, 01 Nov 2019 14:58:49: start model_add_line... INFO @ Fri, 01 Nov 2019 14:58:49: start X-correlation... INFO @ Fri, 01 Nov 2019 14:58:49: end of X-cor INFO @ Fri, 01 Nov 2019 14:58:49: #2 finished! INFO @ Fri, 01 Nov 2019 14:58:49: #2 predicted fragment length is 74 bps INFO @ Fri, 01 Nov 2019 14:58:49: #2 alternative fragment length(s) may be 74,216 bps INFO @ Fri, 01 Nov 2019 14:58:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.20_model.r WARNING @ Fri, 01 Nov 2019 14:58:49: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 14:58:49: #2 You may need to consider one of the other alternative d(s): 74,216 WARNING @ Fri, 01 Nov 2019 14:58:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 01 Nov 2019 14:58:49: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:58:49: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 01 Nov 2019 14:58:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 01 Nov 2019 14:58:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.20_peaks.xls INFO @ Fri, 01 Nov 2019 14:58:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:58:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6370202/SRX6370202.20_summits.bed INFO @ Fri, 01 Nov 2019 14:58:51: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 2 millis CompletedMACS2peakCalling