Job ID = 4287194 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T02:48:39 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 ) 2019-12-10T02:48:39 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 ) 2019-12-10T02:48:39 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 ) 2019-12-10T02:48:39 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 ) 2019-12-10T02:48:39 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 ) 2019-12-10T02:49:13 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 ) 2019-12-10T02:49:13 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.49' 2019-12-10T02:49:13 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 '172.19.7.49' 2019-12-10T02:52:14 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 : 15,675,643 reads read : 31,351,286 reads written : 15,675,643 reads 0-length : 15,675,643 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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:08:39 15675643 reads; of these: 15675643 (100.00%) were unpaired; of these: 9508163 (60.66%) aligned 0 times 4142006 (26.42%) aligned exactly 1 time 2025474 (12.92%) aligned >1 times 39.34% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 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_rmdupse_core] 302603 / 6167480 = 0.0491 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.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 @ Tue, 10 Dec 2019 12:04:58: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:04:58: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:05:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.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 @ Tue, 10 Dec 2019 12:05:05: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:05:05: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:05:07: 1000000 INFO @ Tue, 10 Dec 2019 12:05:16: 1000000 INFO @ Tue, 10 Dec 2019 12:05:17: 2000000 INFO @ Tue, 10 Dec 2019 12:05:26: 3000000 INFO @ Tue, 10 Dec 2019 12:05:27: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:05:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.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 @ Tue, 10 Dec 2019 12:05:36: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:05:36: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:05:38: 4000000 INFO @ Tue, 10 Dec 2019 12:05:44: 3000000 INFO @ Tue, 10 Dec 2019 12:05:51: 5000000 INFO @ Tue, 10 Dec 2019 12:05:55: 1000000 INFO @ Tue, 10 Dec 2019 12:06:03: 4000000 INFO @ Tue, 10 Dec 2019 12:06:05: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:06:05: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:06:05: #1 total tags in treatment: 5864877 INFO @ Tue, 10 Dec 2019 12:06:05: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:06:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:06:05: #1 tags after filtering in treatment: 5864633 INFO @ Tue, 10 Dec 2019 12:06:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:06:05: #1 finished! INFO @ Tue, 10 Dec 2019 12:06:05: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:06:08: #2 number of paired peaks: 8876 INFO @ Tue, 10 Dec 2019 12:06:08: start model_add_line... INFO @ Tue, 10 Dec 2019 12:06:08: start X-correlation... INFO @ Tue, 10 Dec 2019 12:06:08: end of X-cor INFO @ Tue, 10 Dec 2019 12:06:08: #2 finished! INFO @ Tue, 10 Dec 2019 12:06:08: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 12:06:08: #2 alternative fragment length(s) may be 52,129,148,235 bps INFO @ Tue, 10 Dec 2019 12:06:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.05_model.r WARNING @ Tue, 10 Dec 2019 12:06:08: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:06:08: #2 You may need to consider one of the other alternative d(s): 52,129,148,235 WARNING @ Tue, 10 Dec 2019 12:06:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:06:08: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:06:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:06:15: 2000000 INFO @ Tue, 10 Dec 2019 12:06:21: 5000000 INFO @ Tue, 10 Dec 2019 12:06:28: 3000000 INFO @ Tue, 10 Dec 2019 12:06:31: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:06:31: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:06:31: #1 total tags in treatment: 5864877 INFO @ Tue, 10 Dec 2019 12:06:31: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:06:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:06:31: #1 tags after filtering in treatment: 5864633 INFO @ Tue, 10 Dec 2019 12:06:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:06:31: #1 finished! INFO @ Tue, 10 Dec 2019 12:06:31: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:06:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:06:31: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:06:33: #2 number of paired peaks: 8876 INFO @ Tue, 10 Dec 2019 12:06:33: start model_add_line... INFO @ Tue, 10 Dec 2019 12:06:33: start X-correlation... INFO @ Tue, 10 Dec 2019 12:06:33: end of X-cor INFO @ Tue, 10 Dec 2019 12:06:33: #2 finished! INFO @ Tue, 10 Dec 2019 12:06:33: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 12:06:33: #2 alternative fragment length(s) may be 52,129,148,235 bps INFO @ Tue, 10 Dec 2019 12:06:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.10_model.r WARNING @ Tue, 10 Dec 2019 12:06:36: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:06:36: #2 You may need to consider one of the other alternative d(s): 52,129,148,235 WARNING @ Tue, 10 Dec 2019 12:06:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:06:36: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:06:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:06:39: 4000000 INFO @ Tue, 10 Dec 2019 12:06:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:06:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.05_summits.bed INFO @ Tue, 10 Dec 2019 12:06:41: Done! pass1 - making usageList (58 chroms): 2 millis pass2 - checking and writing primary data (739 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:06:49: 5000000 INFO @ Tue, 10 Dec 2019 12:06:55: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:06:58: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:06:58: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:06:58: #1 total tags in treatment: 5864877 INFO @ Tue, 10 Dec 2019 12:06:58: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:06:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:06:58: #1 tags after filtering in treatment: 5864633 INFO @ Tue, 10 Dec 2019 12:06:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:06:58: #1 finished! INFO @ Tue, 10 Dec 2019 12:06:58: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:07:00: #2 number of paired peaks: 8876 INFO @ Tue, 10 Dec 2019 12:07:00: start model_add_line... INFO @ Tue, 10 Dec 2019 12:07:00: start X-correlation... INFO @ Tue, 10 Dec 2019 12:07:00: end of X-cor INFO @ Tue, 10 Dec 2019 12:07:00: #2 finished! INFO @ Tue, 10 Dec 2019 12:07:00: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 12:07:00: #2 alternative fragment length(s) may be 52,129,148,235 bps INFO @ Tue, 10 Dec 2019 12:07:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.20_model.r WARNING @ Tue, 10 Dec 2019 12:07:00: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:07:00: #2 You may need to consider one of the other alternative d(s): 52,129,148,235 WARNING @ Tue, 10 Dec 2019 12:07:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:07:00: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:07:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:07:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:07:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:07:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.10_summits.bed INFO @ Tue, 10 Dec 2019 12:07:04: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (428 records, 4 fields): 3879 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:07:19: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:07:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:07:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:07:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654054/SRX4654054.20_summits.bed INFO @ Tue, 10 Dec 2019 12:07:28: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (171 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。