Job ID = 2001675 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T23:06:07 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 : NET - Reading information from the socket failed ) 2019-07-04T23:06:07 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 : NET - Reading information from the socket failed ) 2019-07-04T23:06:07 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 : NET - Reading information from the socket failed ) 2019-07-04T23:06:07 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 ) 2019-07-04T23:06:07 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 ) 2019-07-04T23:07:48 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 ) 2019-07-04T23:09:12 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 ) 2019-07-04T23:09:12 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 ) spots read : 25,309,253 reads read : 25,309,253 reads written : 25,309,253 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:37 25309253 reads; of these: 25309253 (100.00%) were unpaired; of these: 525934 (2.08%) aligned 0 times 22194890 (87.69%) aligned exactly 1 time 2588429 (10.23%) aligned >1 times 97.92% overall alignment rate Time searching: 00:06:40 Overall time: 00:06:40 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] 11589993 / 24783319 = 0.4677 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 08:23:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.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 08:23:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:23:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:23:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.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 08:23:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:23:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:23:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.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 08:23:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:23:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:23:40: 1000000 INFO @ Fri, 05 Jul 2019 08:23:40: 1000000 INFO @ Fri, 05 Jul 2019 08:23:40: 1000000 INFO @ Fri, 05 Jul 2019 08:23:49: 2000000 INFO @ Fri, 05 Jul 2019 08:23:50: 2000000 INFO @ Fri, 05 Jul 2019 08:23:50: 2000000 INFO @ Fri, 05 Jul 2019 08:23:57: 3000000 INFO @ Fri, 05 Jul 2019 08:24:00: 3000000 INFO @ Fri, 05 Jul 2019 08:24:00: 3000000 INFO @ Fri, 05 Jul 2019 08:24:06: 4000000 INFO @ Fri, 05 Jul 2019 08:24:09: 4000000 INFO @ Fri, 05 Jul 2019 08:24:10: 4000000 INFO @ Fri, 05 Jul 2019 08:24:14: 5000000 INFO @ Fri, 05 Jul 2019 08:24:19: 5000000 INFO @ Fri, 05 Jul 2019 08:24:20: 5000000 INFO @ Fri, 05 Jul 2019 08:24:23: 6000000 INFO @ Fri, 05 Jul 2019 08:24:29: 6000000 INFO @ Fri, 05 Jul 2019 08:24:30: 6000000 INFO @ Fri, 05 Jul 2019 08:24:31: 7000000 INFO @ Fri, 05 Jul 2019 08:24:38: 7000000 INFO @ Fri, 05 Jul 2019 08:24:40: 7000000 INFO @ Fri, 05 Jul 2019 08:24:40: 8000000 INFO @ Fri, 05 Jul 2019 08:24:48: 8000000 INFO @ Fri, 05 Jul 2019 08:24:49: 9000000 INFO @ Fri, 05 Jul 2019 08:24:50: 8000000 INFO @ Fri, 05 Jul 2019 08:24:57: 9000000 INFO @ Fri, 05 Jul 2019 08:24:57: 10000000 INFO @ Fri, 05 Jul 2019 08:25:00: 9000000 INFO @ Fri, 05 Jul 2019 08:25:06: 11000000 INFO @ Fri, 05 Jul 2019 08:25:06: 10000000 INFO @ Fri, 05 Jul 2019 08:25:10: 10000000 INFO @ Fri, 05 Jul 2019 08:25:14: 12000000 INFO @ Fri, 05 Jul 2019 08:25:16: 11000000 INFO @ Fri, 05 Jul 2019 08:25:20: 11000000 INFO @ Fri, 05 Jul 2019 08:25:22: 13000000 INFO @ Fri, 05 Jul 2019 08:25:24: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:25:24: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:25:24: #1 total tags in treatment: 13193326 INFO @ Fri, 05 Jul 2019 08:25:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:25:24: #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 08:25:24: #1 tags after filtering in treatment: 13193082 INFO @ Fri, 05 Jul 2019 08:25:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:25:24: #1 finished! INFO @ Fri, 05 Jul 2019 08:25:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:25:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:25:25: 12000000 INFO @ Fri, 05 Jul 2019 08:25:28: #2 number of paired peaks: 54185 INFO @ Fri, 05 Jul 2019 08:25:28: start model_add_line... INFO @ Fri, 05 Jul 2019 08:25:28: start X-correlation... INFO @ Fri, 05 Jul 2019 08:25:28: end of X-cor INFO @ Fri, 05 Jul 2019 08:25:28: #2 finished! INFO @ Fri, 05 Jul 2019 08:25:28: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 08:25:28: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 08:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.20_model.r INFO @ Fri, 05 Jul 2019 08:25:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:25:29: 12000000 INFO @ Fri, 05 Jul 2019 08:25:35: 13000000 INFO @ Fri, 05 Jul 2019 08:25:36: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:25:36: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:25:36: #1 total tags in treatment: 13193326 INFO @ Fri, 05 Jul 2019 08:25:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:25:36: #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 08:25:37: #1 tags after filtering in treatment: 13193082 INFO @ Fri, 05 Jul 2019 08:25:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:25:37: #1 finished! INFO @ Fri, 05 Jul 2019 08:25:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:25:39: 13000000 INFO @ Fri, 05 Jul 2019 08:25:41: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:25:41: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:25:41: #1 total tags in treatment: 13193326 INFO @ Fri, 05 Jul 2019 08:25:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:25:41: #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 08:25:41: #2 number of paired peaks: 54185 INFO @ Fri, 05 Jul 2019 08:25:41: start model_add_line... INFO @ Fri, 05 Jul 2019 08:25:41: start X-correlation... INFO @ Fri, 05 Jul 2019 08:25:41: end of X-cor INFO @ Fri, 05 Jul 2019 08:25:41: #2 finished! INFO @ Fri, 05 Jul 2019 08:25:41: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 08:25:41: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 08:25:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.05_model.r INFO @ Fri, 05 Jul 2019 08:25:41: #1 tags after filtering in treatment: 13193082 INFO @ Fri, 05 Jul 2019 08:25:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:25:41: #1 finished! INFO @ Fri, 05 Jul 2019 08:25:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:25:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:25:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:25:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:25:45: #2 number of paired peaks: 54185 INFO @ Fri, 05 Jul 2019 08:25:45: start model_add_line... INFO @ Fri, 05 Jul 2019 08:25:45: start X-correlation... INFO @ Fri, 05 Jul 2019 08:25:45: end of X-cor INFO @ Fri, 05 Jul 2019 08:25:45: #2 finished! INFO @ Fri, 05 Jul 2019 08:25:45: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 08:25:45: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 08:25:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.10_model.r INFO @ Fri, 05 Jul 2019 08:25:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:25:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:26:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:26:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:26:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:26:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:26:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:26:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.20_summits.bed INFO @ Fri, 05 Jul 2019 08:26:33: Done! pass1 - making usageList (83 chroms): 8 millis pass2 - checking and writing primary data (22971 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:26:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:26:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.05_summits.bed INFO @ Fri, 05 Jul 2019 08:26:50: Done! INFO @ Fri, 05 Jul 2019 08:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101990/ERX101990.10_summits.bed INFO @ Fri, 05 Jul 2019 08:26:51: Done! pass1 - making usageList (138 chroms): 9 millis pass2 - checking and writing primary data (45967 records, 4 fields): 63 millis pass1 - making usageList (110 chroms): 12 millis pass2 - checking and writing primary data (35364 records, 4 fields): 49 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。