Job ID = 2001560 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:53:44 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 ) 2019-07-04T19:53:44 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 ) 2019-07-04T19:56:01 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 ) 2019-07-04T19:56:01 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 ) 2019-07-04T19:56:01 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 ) 2019-07-04T19:56:21 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 ) 2019-07-04T19:56:23 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 : 26,674,003 reads read : 26,674,003 reads written : 26,674,003 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: 00:11:05 26674003 reads; of these: 26674003 (100.00%) were unpaired; of these: 642685 (2.41%) aligned 0 times 19484960 (73.05%) aligned exactly 1 time 6546358 (24.54%) aligned >1 times 97.59% overall alignment rate Time searching: 00:11:08 Overall time: 00:11:08 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] 1598683 / 26031318 = 0.0614 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 @ Fri, 05 Jul 2019 05:19:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.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 @ Fri, 05 Jul 2019 05:19:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:19:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:19:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.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 @ Fri, 05 Jul 2019 05:19:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:19:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:19:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.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 @ Fri, 05 Jul 2019 05:19:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:19:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:19:45: 1000000 INFO @ Fri, 05 Jul 2019 05:19:46: 1000000 INFO @ Fri, 05 Jul 2019 05:19:46: 1000000 INFO @ Fri, 05 Jul 2019 05:19:52: 2000000 INFO @ Fri, 05 Jul 2019 05:19:54: 2000000 INFO @ Fri, 05 Jul 2019 05:19:56: 2000000 INFO @ Fri, 05 Jul 2019 05:19:59: 3000000 INFO @ Fri, 05 Jul 2019 05:20:02: 3000000 INFO @ Fri, 05 Jul 2019 05:20:05: 3000000 INFO @ Fri, 05 Jul 2019 05:20:06: 4000000 INFO @ Fri, 05 Jul 2019 05:20:09: 4000000 INFO @ Fri, 05 Jul 2019 05:20:13: 5000000 INFO @ Fri, 05 Jul 2019 05:20:14: 4000000 INFO @ Fri, 05 Jul 2019 05:20:18: 5000000 INFO @ Fri, 05 Jul 2019 05:20:20: 6000000 INFO @ Fri, 05 Jul 2019 05:20:23: 5000000 INFO @ Fri, 05 Jul 2019 05:20:25: 6000000 INFO @ Fri, 05 Jul 2019 05:20:27: 7000000 INFO @ Fri, 05 Jul 2019 05:20:32: 6000000 INFO @ Fri, 05 Jul 2019 05:20:32: 7000000 INFO @ Fri, 05 Jul 2019 05:20:34: 8000000 INFO @ Fri, 05 Jul 2019 05:20:40: 8000000 INFO @ Fri, 05 Jul 2019 05:20:41: 7000000 INFO @ Fri, 05 Jul 2019 05:20:42: 9000000 INFO @ Fri, 05 Jul 2019 05:20:47: 9000000 INFO @ Fri, 05 Jul 2019 05:20:50: 8000000 INFO @ Fri, 05 Jul 2019 05:20:50: 10000000 INFO @ Fri, 05 Jul 2019 05:20:55: 10000000 INFO @ Fri, 05 Jul 2019 05:20:58: 11000000 INFO @ Fri, 05 Jul 2019 05:20:59: 9000000 INFO @ Fri, 05 Jul 2019 05:21:03: 11000000 INFO @ Fri, 05 Jul 2019 05:21:06: 12000000 INFO @ Fri, 05 Jul 2019 05:21:07: 10000000 INFO @ Fri, 05 Jul 2019 05:21:11: 12000000 INFO @ Fri, 05 Jul 2019 05:21:14: 13000000 INFO @ Fri, 05 Jul 2019 05:21:16: 11000000 INFO @ Fri, 05 Jul 2019 05:21:18: 13000000 INFO @ Fri, 05 Jul 2019 05:21:21: 14000000 INFO @ Fri, 05 Jul 2019 05:21:25: 12000000 INFO @ Fri, 05 Jul 2019 05:21:26: 14000000 INFO @ Fri, 05 Jul 2019 05:21:29: 15000000 INFO @ Fri, 05 Jul 2019 05:21:34: 15000000 INFO @ Fri, 05 Jul 2019 05:21:34: 13000000 INFO @ Fri, 05 Jul 2019 05:21:37: 16000000 INFO @ Fri, 05 Jul 2019 05:21:42: 16000000 INFO @ Fri, 05 Jul 2019 05:21:43: 14000000 INFO @ Fri, 05 Jul 2019 05:21:46: 17000000 INFO @ Fri, 05 Jul 2019 05:21:51: 17000000 INFO @ Fri, 05 Jul 2019 05:21:51: 15000000 INFO @ Fri, 05 Jul 2019 05:21:54: 18000000 INFO @ Fri, 05 Jul 2019 05:21:59: 18000000 INFO @ Fri, 05 Jul 2019 05:21:59: 16000000 INFO @ Fri, 05 Jul 2019 05:22:02: 19000000 INFO @ Fri, 05 Jul 2019 05:22:07: 19000000 INFO @ Fri, 05 Jul 2019 05:22:08: 17000000 INFO @ Fri, 05 Jul 2019 05:22:10: 20000000 INFO @ Fri, 05 Jul 2019 05:22:15: 20000000 INFO @ Fri, 05 Jul 2019 05:22:17: 18000000 INFO @ Fri, 05 Jul 2019 05:22:18: 21000000 INFO @ Fri, 05 Jul 2019 05:22:24: 21000000 INFO @ Fri, 05 Jul 2019 05:22:25: 19000000 INFO @ Fri, 05 Jul 2019 05:22:26: 22000000 INFO @ Fri, 05 Jul 2019 05:22:32: 22000000 INFO @ Fri, 05 Jul 2019 05:22:34: 20000000 INFO @ Fri, 05 Jul 2019 05:22:34: 23000000 INFO @ Fri, 05 Jul 2019 05:22:40: 23000000 INFO @ Fri, 05 Jul 2019 05:22:42: 24000000 INFO @ Fri, 05 Jul 2019 05:22:42: 21000000 INFO @ Fri, 05 Jul 2019 05:22:45: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:22:45: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:22:45: #1 total tags in treatment: 24432635 INFO @ Fri, 05 Jul 2019 05:22:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:22:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 05:22:46: #1 tags after filtering in treatment: 24432484 INFO @ Fri, 05 Jul 2019 05:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:22:46: #1 finished! INFO @ Fri, 05 Jul 2019 05:22:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:22:47: 24000000 INFO @ Fri, 05 Jul 2019 05:22:51: #2 number of paired peaks: 42594 INFO @ Fri, 05 Jul 2019 05:22:51: start model_add_line... INFO @ Fri, 05 Jul 2019 05:22:51: 22000000 INFO @ Fri, 05 Jul 2019 05:22:51: start X-correlation... INFO @ Fri, 05 Jul 2019 05:22:51: end of X-cor INFO @ Fri, 05 Jul 2019 05:22:51: #2 finished! INFO @ Fri, 05 Jul 2019 05:22:51: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:22:51: #2 alternative fragment length(s) may be 130 bps INFO @ Fri, 05 Jul 2019 05:22:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.10_model.r INFO @ Fri, 05 Jul 2019 05:22:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:22:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:22:51: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:22:51: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:22:51: #1 total tags in treatment: 24432635 INFO @ Fri, 05 Jul 2019 05:22:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:22:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 05:22:52: #1 tags after filtering in treatment: 24432484 INFO @ Fri, 05 Jul 2019 05:22:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:22:52: #1 finished! INFO @ Fri, 05 Jul 2019 05:22:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:22:57: #2 number of paired peaks: 42594 INFO @ Fri, 05 Jul 2019 05:22:57: start model_add_line... INFO @ Fri, 05 Jul 2019 05:22:57: start X-correlation... INFO @ Fri, 05 Jul 2019 05:22:57: end of X-cor INFO @ Fri, 05 Jul 2019 05:22:57: #2 finished! INFO @ Fri, 05 Jul 2019 05:22:57: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:22:57: #2 alternative fragment length(s) may be 130 bps INFO @ Fri, 05 Jul 2019 05:22:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.20_model.r INFO @ Fri, 05 Jul 2019 05:22:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:22:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:22:59: 23000000 INFO @ Fri, 05 Jul 2019 05:23:08: 24000000 INFO @ Fri, 05 Jul 2019 05:23:11: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:23:11: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:23:11: #1 total tags in treatment: 24432635 INFO @ Fri, 05 Jul 2019 05:23:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:23:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 05:23:12: #1 tags after filtering in treatment: 24432484 INFO @ Fri, 05 Jul 2019 05:23:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:23:12: #1 finished! INFO @ Fri, 05 Jul 2019 05:23:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:23:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:23:17: #2 number of paired peaks: 42594 INFO @ Fri, 05 Jul 2019 05:23:17: start model_add_line... INFO @ Fri, 05 Jul 2019 05:23:17: start X-correlation... INFO @ Fri, 05 Jul 2019 05:23:17: end of X-cor INFO @ Fri, 05 Jul 2019 05:23:17: #2 finished! INFO @ Fri, 05 Jul 2019 05:23:17: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:23:17: #2 alternative fragment length(s) may be 130 bps INFO @ Fri, 05 Jul 2019 05:23:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.05_model.r INFO @ Fri, 05 Jul 2019 05:23:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:23:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:24:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:24:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:24:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:24:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:24:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:24:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.10_summits.bed INFO @ Fri, 05 Jul 2019 05:24:53: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (1675 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:25:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:25:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:25:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.20_summits.bed INFO @ Fri, 05 Jul 2019 05:25:01: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (186 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:25:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:25:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:25:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101903/ERX101903.05_summits.bed INFO @ Fri, 05 Jul 2019 05:25:17: Done! pass1 - making usageList (72 chroms): 7 millis pass2 - checking and writing primary data (7018 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。