Job ID = 1294315 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T21:18:37 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 ) 2019-06-02T21:20:46 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 ) 2019-06-02T21:20:46 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 ) 2019-06-02T21:20:56 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 ) 2019-06-02T21:21:21 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 ) 2019-06-02T21:21:21 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.50' 2019-06-02T21:21:21 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 '172.19.7.50' 2019-06-02T21:21:21 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 ) 2019-06-02T21:21:21 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.50' 2019-06-02T21:21:21 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 '172.19.7.50' 2019-06-02T21:21:51 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 ) 2019-06-02T21:21:51 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.50' 2019-06-02T21:21:51 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 '172.19.7.50' 2019-06-02T21:21:51 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 ) 2019-06-02T21:21:51 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.50' 2019-06-02T21:21:51 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra44/SRR/004990/SRR5110256' (130.14.250.27), 32768) from '172.19.7.50' 2019-06-02T21:21:51 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 '172.19.7.50' 2019-06-02T21:21:51 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra44/SRR/004990/SRR5110256' (130.14.250.27), 32768) from '172.19.7.50' 2019-06-02T21:22:45 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 ) 2019-06-02T21:22:45 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 ) 2019-06-02T21:22:45 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.50' 2019-06-02T21:22:45 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.50' 2019-06-02T21:22:45 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 '172.19.7.50' 2019-06-02T21:22:45 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 '172.19.7.50' spots read : 15,954,030 reads read : 15,954,030 reads written : 15,954,030 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: 00:07:38 15954030 reads; of these: 15954030 (100.00%) were unpaired; of these: 369857 (2.32%) aligned 0 times 10877528 (68.18%) aligned exactly 1 time 4706645 (29.50%) aligned >1 times 97.68% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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] 1888441 / 15584173 = 0.1212 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 06:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.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 06:38:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:38:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.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 06:38:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:38:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.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 06:38:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:38:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:39:00: 1000000 INFO @ Mon, 03 Jun 2019 06:39:00: 1000000 INFO @ Mon, 03 Jun 2019 06:39:02: 1000000 INFO @ Mon, 03 Jun 2019 06:39:10: 2000000 INFO @ Mon, 03 Jun 2019 06:39:11: 2000000 INFO @ Mon, 03 Jun 2019 06:39:15: 2000000 INFO @ Mon, 03 Jun 2019 06:39:20: 3000000 INFO @ Mon, 03 Jun 2019 06:39:21: 3000000 INFO @ Mon, 03 Jun 2019 06:39:27: 3000000 INFO @ Mon, 03 Jun 2019 06:39:30: 4000000 INFO @ Mon, 03 Jun 2019 06:39:32: 4000000 INFO @ Mon, 03 Jun 2019 06:39:39: 4000000 INFO @ Mon, 03 Jun 2019 06:39:40: 5000000 INFO @ Mon, 03 Jun 2019 06:39:42: 5000000 INFO @ Mon, 03 Jun 2019 06:39:50: 6000000 INFO @ Mon, 03 Jun 2019 06:39:50: 5000000 INFO @ Mon, 03 Jun 2019 06:39:52: 6000000 INFO @ Mon, 03 Jun 2019 06:40:00: 7000000 INFO @ Mon, 03 Jun 2019 06:40:02: 6000000 INFO @ Mon, 03 Jun 2019 06:40:03: 7000000 INFO @ Mon, 03 Jun 2019 06:40:10: 8000000 INFO @ Mon, 03 Jun 2019 06:40:13: 8000000 INFO @ Mon, 03 Jun 2019 06:40:14: 7000000 INFO @ Mon, 03 Jun 2019 06:40:20: 9000000 INFO @ Mon, 03 Jun 2019 06:40:23: 9000000 INFO @ Mon, 03 Jun 2019 06:40:26: 8000000 INFO @ Mon, 03 Jun 2019 06:40:29: 10000000 INFO @ Mon, 03 Jun 2019 06:40:33: 10000000 INFO @ Mon, 03 Jun 2019 06:40:37: 9000000 INFO @ Mon, 03 Jun 2019 06:40:39: 11000000 INFO @ Mon, 03 Jun 2019 06:40:43: 11000000 INFO @ Mon, 03 Jun 2019 06:40:49: 12000000 INFO @ Mon, 03 Jun 2019 06:40:49: 10000000 INFO @ Mon, 03 Jun 2019 06:40:53: 12000000 INFO @ Mon, 03 Jun 2019 06:40:59: 13000000 INFO @ Mon, 03 Jun 2019 06:41:01: 11000000 INFO @ Mon, 03 Jun 2019 06:41:03: 13000000 INFO @ Mon, 03 Jun 2019 06:41:06: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:41:06: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:41:06: #1 total tags in treatment: 13695732 INFO @ Mon, 03 Jun 2019 06:41:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:41:06: #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 06:41:06: #1 tags after filtering in treatment: 13695732 INFO @ Mon, 03 Jun 2019 06:41:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:41:06: #1 finished! INFO @ Mon, 03 Jun 2019 06:41:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:41:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:41:07: #2 number of paired peaks: 982 WARNING @ Mon, 03 Jun 2019 06:41:07: Fewer paired peaks (982) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 982 pairs to build model! INFO @ Mon, 03 Jun 2019 06:41:07: start model_add_line... INFO @ Mon, 03 Jun 2019 06:41:07: start X-correlation... INFO @ Mon, 03 Jun 2019 06:41:07: end of X-cor INFO @ Mon, 03 Jun 2019 06:41:07: #2 finished! INFO @ Mon, 03 Jun 2019 06:41:07: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 06:41:07: #2 alternative fragment length(s) may be 4,63 bps INFO @ Mon, 03 Jun 2019 06:41:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.05_model.r WARNING @ Mon, 03 Jun 2019 06:41:08: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:41:08: #2 You may need to consider one of the other alternative d(s): 4,63 WARNING @ Mon, 03 Jun 2019 06:41:08: #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 06:41:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:41:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:41:10: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:41:10: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:41:10: #1 total tags in treatment: 13695732 INFO @ Mon, 03 Jun 2019 06:41:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:41:10: #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 06:41:10: #1 tags after filtering in treatment: 13695732 INFO @ Mon, 03 Jun 2019 06:41:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:41:10: #1 finished! INFO @ Mon, 03 Jun 2019 06:41:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:41:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:41:12: #2 number of paired peaks: 982 WARNING @ Mon, 03 Jun 2019 06:41:12: Fewer paired peaks (982) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 982 pairs to build model! INFO @ Mon, 03 Jun 2019 06:41:12: start model_add_line... INFO @ Mon, 03 Jun 2019 06:41:12: start X-correlation... INFO @ Mon, 03 Jun 2019 06:41:12: end of X-cor INFO @ Mon, 03 Jun 2019 06:41:12: #2 finished! INFO @ Mon, 03 Jun 2019 06:41:12: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 06:41:12: #2 alternative fragment length(s) may be 4,63 bps INFO @ Mon, 03 Jun 2019 06:41:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.20_model.r WARNING @ Mon, 03 Jun 2019 06:41:12: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:41:12: #2 You may need to consider one of the other alternative d(s): 4,63 WARNING @ Mon, 03 Jun 2019 06:41:12: #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 06:41:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:41:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:41:12: 12000000 INFO @ Mon, 03 Jun 2019 06:41:23: 13000000 INFO @ Mon, 03 Jun 2019 06:41:31: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:41:31: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:41:31: #1 total tags in treatment: 13695732 INFO @ Mon, 03 Jun 2019 06:41:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:41:31: #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 06:41:31: #1 tags after filtering in treatment: 13695732 INFO @ Mon, 03 Jun 2019 06:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:41:31: #1 finished! INFO @ Mon, 03 Jun 2019 06:41:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:41:32: #2 number of paired peaks: 982 WARNING @ Mon, 03 Jun 2019 06:41:32: Fewer paired peaks (982) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 982 pairs to build model! INFO @ Mon, 03 Jun 2019 06:41:32: start model_add_line... INFO @ Mon, 03 Jun 2019 06:41:33: start X-correlation... INFO @ Mon, 03 Jun 2019 06:41:33: end of X-cor INFO @ Mon, 03 Jun 2019 06:41:33: #2 finished! INFO @ Mon, 03 Jun 2019 06:41:33: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 06:41:33: #2 alternative fragment length(s) may be 4,63 bps INFO @ Mon, 03 Jun 2019 06:41:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.10_model.r WARNING @ Mon, 03 Jun 2019 06:41:33: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:41:33: #2 You may need to consider one of the other alternative d(s): 4,63 WARNING @ Mon, 03 Jun 2019 06:41:33: #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 06:41:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:41:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:41:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:41:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:42:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:42:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:42:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.05_summits.bed INFO @ Mon, 03 Jun 2019 06:42:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3423 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:42:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:42:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:42:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.20_summits.bed INFO @ Mon, 03 Jun 2019 06:42:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (868 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:42:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:42:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:42:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:42:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422642/SRX2422642.10_summits.bed INFO @ Mon, 03 Jun 2019 06:42:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1688 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。