Job ID = 3785834 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:33:42 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 ) 2019-11-01T05:33:42 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 ) 2019-11-01T05:36:06 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 ) 2019-11-01T05:36:12 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 ) 2019-11-01T05:36:12 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 ) 2019-11-01T05:37:56 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:39:29 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 ) 2019-11-01T05:39:29 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 ) 2019-11-01T05:39:36 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 ) 2019-11-01T05:41:14 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 ) 2019-11-01T05:41:53 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 ) 2019-11-01T05:43:21 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 ) 2019-11-01T05:43:32 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 ) 2019-11-01T05:44:44 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 ) 2019-11-01T05:44:44 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 ) 2019-11-01T05:45:15 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 ) 2019-11-01T05:45:15 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 ) 2019-11-01T05:45:36 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 ) 2019-11-01T05:45:55 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 ) 2019-11-01T05:46:13 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 ) 2019-11-01T05:46:37 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 ) 2019-11-01T05:47:13 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 ) 2019-11-01T05:47:13 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 ) 2019-11-01T05:47:53 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 ) 2019-11-01T05:47:53 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 ) 2019-11-01T05:48:30 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 ) 2019-11-01T05:48:51 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 ) 2019-11-01T05:50:02 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 ) 2019-11-01T05:50:17 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 ) 2019-11-01T05:50:46 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 ) 2019-11-01T05:50:46 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 ) 2019-11-01T05:52:21 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 ) 2019-11-01T05:53:28 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 ) 2019-11-01T05:55:22 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 ) 2019-11-01T05:55:22 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 ) 2019-11-01T05:55:42 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 ) 2019-11-01T05:56:08 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 ) 2019-11-01T05:56:08 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 ) 2019-11-01T05:56:15 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 ) 2019-11-01T05:57:58 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 ) 2019-11-01T05:58:12 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 ) 2019-11-01T05:59:32 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 ) 2019-11-01T05:59:32 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 ) 2019-11-01T05:59:32 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 ) 2019-11-01T05:59:54 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 ) 2019-11-01T06:04:47 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 ) 2019-11-01T06:07:27 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 : 64,997,012 reads read : 64,997,012 reads written : 64,997,012 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: 00:08:06 64997012 reads; of these: 64997012 (100.00%) were unpaired; of these: 63827768 (98.20%) aligned 0 times 646925 (1.00%) aligned exactly 1 time 522319 (0.80%) aligned >1 times 1.80% overall alignment rate Time searching: 00:08:06 Overall time: 00:08:06 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] 300763 / 1169244 = 0.2572 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 15:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.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 15:29:20: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:29:20: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:29:26: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:29:26: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:29:26: #1 total tags in treatment: 868481 INFO @ Fri, 01 Nov 2019 15:29:26: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:29:26: #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 15:29:26: #1 tags after filtering in treatment: 868481 INFO @ Fri, 01 Nov 2019 15:29:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:29:26: #1 finished! INFO @ Fri, 01 Nov 2019 15:29:26: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:29:26: #2 number of paired peaks: 2266 INFO @ Fri, 01 Nov 2019 15:29:26: start model_add_line... INFO @ Fri, 01 Nov 2019 15:29:26: start X-correlation... INFO @ Fri, 01 Nov 2019 15:29:26: end of X-cor INFO @ Fri, 01 Nov 2019 15:29:26: #2 finished! INFO @ Fri, 01 Nov 2019 15:29:26: #2 predicted fragment length is 48 bps INFO @ Fri, 01 Nov 2019 15:29:26: #2 alternative fragment length(s) may be 48,525 bps INFO @ Fri, 01 Nov 2019 15:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.05_model.r WARNING @ Fri, 01 Nov 2019 15:29:26: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 15:29:26: #2 You may need to consider one of the other alternative d(s): 48,525 WARNING @ Fri, 01 Nov 2019 15:29:26: #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 15:29:26: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:29:29: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:29:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.05_peaks.xls INFO @ Fri, 01 Nov 2019 15:29:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:29:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.05_summits.bed INFO @ Fri, 01 Nov 2019 15:29:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1319 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 15:29:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.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 15:29:50: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:29:50: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:29:56: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:29:56: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:29:56: #1 total tags in treatment: 868481 INFO @ Fri, 01 Nov 2019 15:29:56: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:29:56: #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 15:29:56: #1 tags after filtering in treatment: 868481 INFO @ Fri, 01 Nov 2019 15:29:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:29:56: #1 finished! INFO @ Fri, 01 Nov 2019 15:29:56: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:29:57: #2 number of paired peaks: 2266 INFO @ Fri, 01 Nov 2019 15:29:57: start model_add_line... INFO @ Fri, 01 Nov 2019 15:29:57: start X-correlation... INFO @ Fri, 01 Nov 2019 15:29:57: end of X-cor INFO @ Fri, 01 Nov 2019 15:29:57: #2 finished! INFO @ Fri, 01 Nov 2019 15:29:57: #2 predicted fragment length is 48 bps INFO @ Fri, 01 Nov 2019 15:29:57: #2 alternative fragment length(s) may be 48,525 bps INFO @ Fri, 01 Nov 2019 15:29:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.10_model.r WARNING @ Fri, 01 Nov 2019 15:29:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 15:29:57: #2 You may need to consider one of the other alternative d(s): 48,525 WARNING @ Fri, 01 Nov 2019 15:29:57: #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 15:29:57: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:29:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:29:59: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:30:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.10_peaks.xls INFO @ Fri, 01 Nov 2019 15:30:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:30:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.10_summits.bed INFO @ Fri, 01 Nov 2019 15:30:01: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (759 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Fri, 01 Nov 2019 15:30:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.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 15:30:20: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:30:20: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:30:28: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:30:28: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:30:28: #1 total tags in treatment: 868481 INFO @ Fri, 01 Nov 2019 15:30:28: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:30:28: #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 15:30:28: #1 tags after filtering in treatment: 868481 INFO @ Fri, 01 Nov 2019 15:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:30:28: #1 finished! INFO @ Fri, 01 Nov 2019 15:30:28: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:30:28: #2 number of paired peaks: 2266 INFO @ Fri, 01 Nov 2019 15:30:28: start model_add_line... INFO @ Fri, 01 Nov 2019 15:30:28: start X-correlation... INFO @ Fri, 01 Nov 2019 15:30:28: end of X-cor INFO @ Fri, 01 Nov 2019 15:30:28: #2 finished! INFO @ Fri, 01 Nov 2019 15:30:28: #2 predicted fragment length is 48 bps INFO @ Fri, 01 Nov 2019 15:30:28: #2 alternative fragment length(s) may be 48,525 bps INFO @ Fri, 01 Nov 2019 15:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.20_model.r WARNING @ Fri, 01 Nov 2019 15:30:28: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 15:30:28: #2 You may need to consider one of the other alternative d(s): 48,525 WARNING @ Fri, 01 Nov 2019 15:30:28: #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 15:30:28: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:30:31: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:30:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.20_peaks.xls INFO @ Fri, 01 Nov 2019 15:30:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:30:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4579166/SRX4579166.20_summits.bed INFO @ Fri, 01 Nov 2019 15:30:32: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (390 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。