Job ID = 2640418 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:34:08 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 ) 2019-08-24T07:34:19 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 ) 2019-08-24T07:34:19 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 ) 2019-08-24T07:34:19 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 ) 2019-08-24T07:35:32 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 ) 2019-08-24T07:35:32 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 ) 2019-08-24T07:35:32 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 ) spots read : 36,773,157 reads read : 36,773,157 reads written : 36,773,157 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: 00:18:09 36773157 reads; of these: 36773157 (100.00%) were unpaired; of these: 10223508 (27.80%) aligned 0 times 17913868 (48.71%) aligned exactly 1 time 8635781 (23.48%) aligned >1 times 72.20% overall alignment rate Time searching: 00:18:12 Overall time: 00:18:13 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 8 files... [bam_rmdupse_core] 7966910 / 26549649 = 0.3001 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:13:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.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 17:13:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:13:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:13:39: 1000000 INFO @ Sat, 24 Aug 2019 17:13:47: 2000000 INFO @ Sat, 24 Aug 2019 17:13:55: 3000000 INFO @ Sat, 24 Aug 2019 17:14:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.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 17:14:00: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:14:00: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:14:03: 4000000 INFO @ Sat, 24 Aug 2019 17:14:08: 1000000 INFO @ Sat, 24 Aug 2019 17:14:11: 5000000 INFO @ Sat, 24 Aug 2019 17:14:15: 2000000 INFO @ Sat, 24 Aug 2019 17:14:19: 6000000 INFO @ Sat, 24 Aug 2019 17:14:23: 3000000 INFO @ Sat, 24 Aug 2019 17:14:27: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:14:30: 4000000 INFO @ Sat, 24 Aug 2019 17:14:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.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 17:14:30: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:14:30: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:14:35: 8000000 INFO @ Sat, 24 Aug 2019 17:14:37: 1000000 INFO @ Sat, 24 Aug 2019 17:14:38: 5000000 INFO @ Sat, 24 Aug 2019 17:14:43: 9000000 INFO @ Sat, 24 Aug 2019 17:14:44: 2000000 INFO @ Sat, 24 Aug 2019 17:14:46: 6000000 INFO @ Sat, 24 Aug 2019 17:14:51: 3000000 INFO @ Sat, 24 Aug 2019 17:14:51: 10000000 INFO @ Sat, 24 Aug 2019 17:14:54: 7000000 INFO @ Sat, 24 Aug 2019 17:14:57: 4000000 INFO @ Sat, 24 Aug 2019 17:14:59: 11000000 INFO @ Sat, 24 Aug 2019 17:15:02: 8000000 INFO @ Sat, 24 Aug 2019 17:15:04: 5000000 INFO @ Sat, 24 Aug 2019 17:15:07: 12000000 INFO @ Sat, 24 Aug 2019 17:15:11: 9000000 INFO @ Sat, 24 Aug 2019 17:15:11: 6000000 INFO @ Sat, 24 Aug 2019 17:15:15: 13000000 INFO @ Sat, 24 Aug 2019 17:15:17: 7000000 INFO @ Sat, 24 Aug 2019 17:15:19: 10000000 INFO @ Sat, 24 Aug 2019 17:15:23: 14000000 INFO @ Sat, 24 Aug 2019 17:15:24: 8000000 INFO @ Sat, 24 Aug 2019 17:15:27: 11000000 INFO @ Sat, 24 Aug 2019 17:15:31: 9000000 INFO @ Sat, 24 Aug 2019 17:15:31: 15000000 INFO @ Sat, 24 Aug 2019 17:15:35: 12000000 INFO @ Sat, 24 Aug 2019 17:15:38: 10000000 INFO @ Sat, 24 Aug 2019 17:15:39: 16000000 INFO @ Sat, 24 Aug 2019 17:15:43: 13000000 INFO @ Sat, 24 Aug 2019 17:15:44: 11000000 INFO @ Sat, 24 Aug 2019 17:15:47: 17000000 INFO @ Sat, 24 Aug 2019 17:15:51: 12000000 INFO @ Sat, 24 Aug 2019 17:15:52: 14000000 INFO @ Sat, 24 Aug 2019 17:15:55: 18000000 INFO @ Sat, 24 Aug 2019 17:15:57: 13000000 INFO @ Sat, 24 Aug 2019 17:16:00: 15000000 INFO @ Sat, 24 Aug 2019 17:16:00: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:16:00: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:16:00: #1 total tags in treatment: 18582739 INFO @ Sat, 24 Aug 2019 17:16:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:16:00: #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 17:16:01: #1 tags after filtering in treatment: 18582599 INFO @ Sat, 24 Aug 2019 17:16:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:16:01: #1 finished! INFO @ Sat, 24 Aug 2019 17:16:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:16:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:16:03: #2 number of paired peaks: 10900 INFO @ Sat, 24 Aug 2019 17:16:03: start model_add_line... INFO @ Sat, 24 Aug 2019 17:16:04: start X-correlation... INFO @ Sat, 24 Aug 2019 17:16:04: end of X-cor INFO @ Sat, 24 Aug 2019 17:16:04: #2 finished! INFO @ Sat, 24 Aug 2019 17:16:04: #2 predicted fragment length is 42 bps INFO @ Sat, 24 Aug 2019 17:16:04: #2 alternative fragment length(s) may be 42,574 bps INFO @ Sat, 24 Aug 2019 17:16:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.05_model.r WARNING @ Sat, 24 Aug 2019 17:16:04: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:16:04: #2 You may need to consider one of the other alternative d(s): 42,574 WARNING @ Sat, 24 Aug 2019 17:16:04: #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 17:16:04: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:16:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:16:04: 14000000 INFO @ Sat, 24 Aug 2019 17:16:08: 16000000 INFO @ Sat, 24 Aug 2019 17:16:11: 15000000 INFO @ Sat, 24 Aug 2019 17:16:16: 17000000 INFO @ Sat, 24 Aug 2019 17:16:17: 16000000 INFO @ Sat, 24 Aug 2019 17:16:24: 17000000 INFO @ Sat, 24 Aug 2019 17:16:24: 18000000 INFO @ Sat, 24 Aug 2019 17:16:29: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:16:29: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:16:29: #1 total tags in treatment: 18582739 INFO @ Sat, 24 Aug 2019 17:16:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:16:29: #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 17:16:30: #1 tags after filtering in treatment: 18582599 INFO @ Sat, 24 Aug 2019 17:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:16:30: #1 finished! INFO @ Sat, 24 Aug 2019 17:16:30: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:16:31: 18000000 INFO @ Sat, 24 Aug 2019 17:16:32: #2 number of paired peaks: 10900 INFO @ Sat, 24 Aug 2019 17:16:32: start model_add_line... INFO @ Sat, 24 Aug 2019 17:16:32: start X-correlation... INFO @ Sat, 24 Aug 2019 17:16:32: end of X-cor INFO @ Sat, 24 Aug 2019 17:16:32: #2 finished! INFO @ Sat, 24 Aug 2019 17:16:32: #2 predicted fragment length is 42 bps INFO @ Sat, 24 Aug 2019 17:16:32: #2 alternative fragment length(s) may be 42,574 bps INFO @ Sat, 24 Aug 2019 17:16:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.10_model.r WARNING @ Sat, 24 Aug 2019 17:16:32: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:16:32: #2 You may need to consider one of the other alternative d(s): 42,574 WARNING @ Sat, 24 Aug 2019 17:16:32: #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 17:16:32: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:16:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:16:35: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:16:35: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:16:35: #1 total tags in treatment: 18582739 INFO @ Sat, 24 Aug 2019 17:16:35: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:16:35: #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 17:16:35: #1 tags after filtering in treatment: 18582599 INFO @ Sat, 24 Aug 2019 17:16:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:16:35: #1 finished! INFO @ Sat, 24 Aug 2019 17:16:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:16:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:16:38: #2 number of paired peaks: 10900 INFO @ Sat, 24 Aug 2019 17:16:38: start model_add_line... INFO @ Sat, 24 Aug 2019 17:16:38: start X-correlation... INFO @ Sat, 24 Aug 2019 17:16:38: end of X-cor INFO @ Sat, 24 Aug 2019 17:16:38: #2 finished! INFO @ Sat, 24 Aug 2019 17:16:38: #2 predicted fragment length is 42 bps INFO @ Sat, 24 Aug 2019 17:16:38: #2 alternative fragment length(s) may be 42,574 bps INFO @ Sat, 24 Aug 2019 17:16:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.20_model.r WARNING @ Sat, 24 Aug 2019 17:16:38: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:16:38: #2 You may need to consider one of the other alternative d(s): 42,574 WARNING @ Sat, 24 Aug 2019 17:16:38: #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 17:16:38: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:16:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:17:02: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:17:30: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:17:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:17:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:17:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.05_summits.bed INFO @ Sat, 24 Aug 2019 17:17:31: Done! pass1 - making usageList (84 chroms): 3 millis pass2 - checking and writing primary data (2740 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:17:36: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:17:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:17:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:17:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.10_summits.bed INFO @ Sat, 24 Aug 2019 17:17:59: Done! pass1 - making usageList (65 chroms): 2 millis pass2 - checking and writing primary data (1395 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:18:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:18:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:18:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208968/SRX208968.20_summits.bed INFO @ Sat, 24 Aug 2019 17:18:05: Done! pass1 - making usageList (55 chroms): 2 millis pass2 - checking and writing primary data (647 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。