Job ID = 2640453 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:51:34 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 ) 2019-08-24T07:51:34 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 ) 2019-08-24T07:52:37 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 ) 2019-08-24T07:52:37 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 ) 2019-08-24T07:53:03 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 ) 2019-08-24T07:54:06 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 ) 2019-08-24T07:57:06 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 ) 2019-08-24T07:59:14 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 ) 2019-08-24T08:00:28 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 ) 2019-08-24T08:01:40 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 ) 2019-08-24T08:07:47 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 ) 2019-08-24T08:07:48 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 ) 2019-08-24T08:07:48 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 ) 2019-08-24T08:08:51 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 ) 2019-08-24T08:10:04 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 ) 2019-08-24T08:12:10 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 ) 2019-08-24T08:14:21 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 ) 2019-08-24T08:14:21 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 ) 2019-08-24T08:14:45 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 ) 2019-08-24T08:14:59 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 ) 2019-08-24T08:14:59 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.58' 2019-08-24T08:14:59 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' (130.14.250.26) from '172.19.7.58' 2019-08-24T08:17:27 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 ) 2019-08-24T08:28:28 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 ) 2019-08-24T08:41:09 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 ) 2019-08-24T08:42:20 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 ) 2019-08-24T08:46:02 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 ) 2019-08-24T08:48:43 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 ) 2019-08-24T08:48:43 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.58' 2019-08-24T08:48:43 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' (130.14.250.24) from '172.19.7.58' 2019-08-24T09:01:53 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 ) 2019-08-24T09:19:29 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 : 406,088,147 reads read : 812,176,294 reads written : 406,088,147 reads 0-length : 406,088,147 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:06:33 406088147 reads; of these: 406088147 (100.00%) were unpaired; of these: 344797283 (84.91%) aligned 0 times 35689619 (8.79%) aligned exactly 1 time 25601245 (6.30%) aligned >1 times 15.09% overall alignment rate Time searching: 01:06:36 Overall time: 01:06:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 50861290 / 61290864 = 0.8298 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:45:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 19:45:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:45:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:45:43: 1000000 INFO @ Sat, 24 Aug 2019 19:45:51: 2000000 INFO @ Sat, 24 Aug 2019 19:45:58: 3000000 INFO @ Sat, 24 Aug 2019 19:46:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 19:46:05: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:46:05: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:46:05: 4000000 INFO @ Sat, 24 Aug 2019 19:46:12: 1000000 INFO @ Sat, 24 Aug 2019 19:46:13: 5000000 INFO @ Sat, 24 Aug 2019 19:46:19: 2000000 INFO @ Sat, 24 Aug 2019 19:46:20: 6000000 INFO @ Sat, 24 Aug 2019 19:46:26: 3000000 INFO @ Sat, 24 Aug 2019 19:46:28: 7000000 INFO @ Sat, 24 Aug 2019 19:46:32: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:46:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 19:46:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:46:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:46:36: 8000000 INFO @ Sat, 24 Aug 2019 19:46:39: 5000000 INFO @ Sat, 24 Aug 2019 19:46:43: 1000000 INFO @ Sat, 24 Aug 2019 19:46:44: 9000000 INFO @ Sat, 24 Aug 2019 19:46:46: 6000000 INFO @ Sat, 24 Aug 2019 19:46:51: 2000000 INFO @ Sat, 24 Aug 2019 19:46:51: 10000000 INFO @ Sat, 24 Aug 2019 19:46:53: 7000000 INFO @ Sat, 24 Aug 2019 19:46:55: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:46:55: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:46:55: #1 total tags in treatment: 10429574 INFO @ Sat, 24 Aug 2019 19:46:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:46:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:46:55: #1 tags after filtering in treatment: 10429410 INFO @ Sat, 24 Aug 2019 19:46:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:46:55: #1 finished! INFO @ Sat, 24 Aug 2019 19:46:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:46:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:46:58: #2 number of paired peaks: 10078 INFO @ Sat, 24 Aug 2019 19:46:58: start model_add_line... INFO @ Sat, 24 Aug 2019 19:46:58: start X-correlation... INFO @ Sat, 24 Aug 2019 19:46:58: end of X-cor INFO @ Sat, 24 Aug 2019 19:46:58: #2 finished! INFO @ Sat, 24 Aug 2019 19:46:58: #2 predicted fragment length is 48 bps INFO @ Sat, 24 Aug 2019 19:46:58: #2 alternative fragment length(s) may be 48,92 bps INFO @ Sat, 24 Aug 2019 19:46:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.05_model.r WARNING @ Sat, 24 Aug 2019 19:46:58: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:46:58: #2 You may need to consider one of the other alternative d(s): 48,92 WARNING @ Sat, 24 Aug 2019 19:46:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:46:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:46:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:46:58: 3000000 INFO @ Sat, 24 Aug 2019 19:47:00: 8000000 INFO @ Sat, 24 Aug 2019 19:47:06: 4000000 INFO @ Sat, 24 Aug 2019 19:47:07: 9000000 INFO @ Sat, 24 Aug 2019 19:47:14: 10000000 INFO @ Sat, 24 Aug 2019 19:47:14: 5000000 INFO @ Sat, 24 Aug 2019 19:47:17: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:47:17: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:47:17: #1 total tags in treatment: 10429574 INFO @ Sat, 24 Aug 2019 19:47:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:47:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:47:17: #1 tags after filtering in treatment: 10429410 INFO @ Sat, 24 Aug 2019 19:47:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:47:17: #1 finished! INFO @ Sat, 24 Aug 2019 19:47:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:47:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:47:20: #2 number of paired peaks: 10078 INFO @ Sat, 24 Aug 2019 19:47:20: start model_add_line... INFO @ Sat, 24 Aug 2019 19:47:20: start X-correlation... INFO @ Sat, 24 Aug 2019 19:47:20: end of X-cor INFO @ Sat, 24 Aug 2019 19:47:20: #2 finished! INFO @ Sat, 24 Aug 2019 19:47:20: #2 predicted fragment length is 48 bps INFO @ Sat, 24 Aug 2019 19:47:20: #2 alternative fragment length(s) may be 48,92 bps INFO @ Sat, 24 Aug 2019 19:47:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.10_model.r WARNING @ Sat, 24 Aug 2019 19:47:20: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:47:20: #2 You may need to consider one of the other alternative d(s): 48,92 WARNING @ Sat, 24 Aug 2019 19:47:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:47:20: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:47:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:47:21: 6000000 INFO @ Sat, 24 Aug 2019 19:47:29: 7000000 INFO @ Sat, 24 Aug 2019 19:47:30: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:47:36: 8000000 INFO @ Sat, 24 Aug 2019 19:47:45: 9000000 INFO @ Sat, 24 Aug 2019 19:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.05_summits.bed INFO @ Sat, 24 Aug 2019 19:47:46: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (409 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:47:52: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:47:52: 10000000 INFO @ Sat, 24 Aug 2019 19:47:55: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:47:55: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:47:55: #1 total tags in treatment: 10429574 INFO @ Sat, 24 Aug 2019 19:47:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:47:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:47:56: #1 tags after filtering in treatment: 10429410 INFO @ Sat, 24 Aug 2019 19:47:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:47:56: #1 finished! INFO @ Sat, 24 Aug 2019 19:47:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:47:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:47:58: #2 number of paired peaks: 10078 INFO @ Sat, 24 Aug 2019 19:47:58: start model_add_line... INFO @ Sat, 24 Aug 2019 19:47:58: start X-correlation... INFO @ Sat, 24 Aug 2019 19:47:58: end of X-cor INFO @ Sat, 24 Aug 2019 19:47:58: #2 finished! INFO @ Sat, 24 Aug 2019 19:47:58: #2 predicted fragment length is 48 bps INFO @ Sat, 24 Aug 2019 19:47:58: #2 alternative fragment length(s) may be 48,92 bps INFO @ Sat, 24 Aug 2019 19:47:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.20_model.r WARNING @ Sat, 24 Aug 2019 19:47:58: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:47:58: #2 You may need to consider one of the other alternative d(s): 48,92 WARNING @ Sat, 24 Aug 2019 19:47:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:47:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:47:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:48:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:48:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:48:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.10_summits.bed INFO @ Sat, 24 Aug 2019 19:48:08: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:48:31: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:48:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:48:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:48:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094895/SRX5094895.20_summits.bed INFO @ Sat, 24 Aug 2019 19:48:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。