Job ID = 2001653 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T22:04:58 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 ) 2019-07-04T22:10:07 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 ) 2019-07-04T22:12:15 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 ) spots read : 21,362,716 reads read : 21,362,716 reads written : 21,362,716 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:01 21362716 reads; of these: 21362716 (100.00%) were unpaired; of these: 454588 (2.13%) aligned 0 times 18400249 (86.13%) aligned exactly 1 time 2507879 (11.74%) aligned >1 times 97.87% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 8994810 / 20908128 = 0.4302 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 07:26:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.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 07:26:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:26:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:26:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.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 07:26:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:26:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.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 07:26:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:26:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:26:20: 1000000 INFO @ Fri, 05 Jul 2019 07:26:21: 1000000 INFO @ Fri, 05 Jul 2019 07:26:23: 1000000 INFO @ Fri, 05 Jul 2019 07:26:27: 2000000 INFO @ Fri, 05 Jul 2019 07:26:28: 2000000 INFO @ Fri, 05 Jul 2019 07:26:30: 2000000 INFO @ Fri, 05 Jul 2019 07:26:33: 3000000 INFO @ Fri, 05 Jul 2019 07:26:34: 3000000 INFO @ Fri, 05 Jul 2019 07:26:36: 3000000 INFO @ Fri, 05 Jul 2019 07:26:39: 4000000 INFO @ Fri, 05 Jul 2019 07:26:40: 4000000 INFO @ Fri, 05 Jul 2019 07:26:43: 4000000 INFO @ Fri, 05 Jul 2019 07:26:45: 5000000 INFO @ Fri, 05 Jul 2019 07:26:46: 5000000 INFO @ Fri, 05 Jul 2019 07:26:50: 5000000 INFO @ Fri, 05 Jul 2019 07:26:51: 6000000 INFO @ Fri, 05 Jul 2019 07:26:52: 6000000 INFO @ Fri, 05 Jul 2019 07:26:56: 6000000 INFO @ Fri, 05 Jul 2019 07:26:57: 7000000 INFO @ Fri, 05 Jul 2019 07:26:58: 7000000 INFO @ Fri, 05 Jul 2019 07:27:03: 7000000 INFO @ Fri, 05 Jul 2019 07:27:03: 8000000 INFO @ Fri, 05 Jul 2019 07:27:04: 8000000 INFO @ Fri, 05 Jul 2019 07:27:09: 9000000 INFO @ Fri, 05 Jul 2019 07:27:09: 8000000 INFO @ Fri, 05 Jul 2019 07:27:10: 9000000 INFO @ Fri, 05 Jul 2019 07:27:15: 10000000 INFO @ Fri, 05 Jul 2019 07:27:16: 10000000 INFO @ Fri, 05 Jul 2019 07:27:16: 9000000 INFO @ Fri, 05 Jul 2019 07:27:21: 11000000 INFO @ Fri, 05 Jul 2019 07:27:22: 11000000 INFO @ Fri, 05 Jul 2019 07:27:23: 10000000 INFO @ Fri, 05 Jul 2019 07:27:27: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:27:27: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:27:27: #1 total tags in treatment: 11913318 INFO @ Fri, 05 Jul 2019 07:27:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:27:27: #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 07:27:27: #1 tags after filtering in treatment: 11913063 INFO @ Fri, 05 Jul 2019 07:27:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:27:27: #1 finished! INFO @ Fri, 05 Jul 2019 07:27:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:27:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:27:27: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:27:27: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:27:27: #1 total tags in treatment: 11913318 INFO @ Fri, 05 Jul 2019 07:27:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:27:27: #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 07:27:28: #1 tags after filtering in treatment: 11913063 INFO @ Fri, 05 Jul 2019 07:27:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:27:28: #1 finished! INFO @ Fri, 05 Jul 2019 07:27:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:27:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:27:29: 11000000 INFO @ Fri, 05 Jul 2019 07:27:31: #2 number of paired peaks: 53038 INFO @ Fri, 05 Jul 2019 07:27:31: start model_add_line... INFO @ Fri, 05 Jul 2019 07:27:31: start X-correlation... INFO @ Fri, 05 Jul 2019 07:27:31: end of X-cor INFO @ Fri, 05 Jul 2019 07:27:31: #2 finished! INFO @ Fri, 05 Jul 2019 07:27:31: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 07:27:31: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 05 Jul 2019 07:27:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.05_model.r INFO @ Fri, 05 Jul 2019 07:27:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:27:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:27:31: #2 number of paired peaks: 53038 INFO @ Fri, 05 Jul 2019 07:27:31: start model_add_line... INFO @ Fri, 05 Jul 2019 07:27:32: start X-correlation... INFO @ Fri, 05 Jul 2019 07:27:32: end of X-cor INFO @ Fri, 05 Jul 2019 07:27:32: #2 finished! INFO @ Fri, 05 Jul 2019 07:27:32: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 07:27:32: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 05 Jul 2019 07:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.10_model.r INFO @ Fri, 05 Jul 2019 07:27:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:27:35: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:27:35: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:27:35: #1 total tags in treatment: 11913318 INFO @ Fri, 05 Jul 2019 07:27:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:27:35: #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 07:27:36: #1 tags after filtering in treatment: 11913063 INFO @ Fri, 05 Jul 2019 07:27:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:27:36: #1 finished! INFO @ Fri, 05 Jul 2019 07:27:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:27:39: #2 number of paired peaks: 53038 INFO @ Fri, 05 Jul 2019 07:27:39: start model_add_line... INFO @ Fri, 05 Jul 2019 07:27:39: start X-correlation... INFO @ Fri, 05 Jul 2019 07:27:39: end of X-cor INFO @ Fri, 05 Jul 2019 07:27:39: #2 finished! INFO @ Fri, 05 Jul 2019 07:27:39: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 07:27:39: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 05 Jul 2019 07:27:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.20_model.r INFO @ Fri, 05 Jul 2019 07:27:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:27:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:28:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:28:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:28:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:28:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:28:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:28:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.05_summits.bed INFO @ Fri, 05 Jul 2019 07:28:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.10_summits.bed INFO @ Fri, 05 Jul 2019 07:28:27: Done! INFO @ Fri, 05 Jul 2019 07:28:28: Done! pass1 - making usageList (101 chroms): 7 millis pass2 - checking and writing primary data (29686 records, 4 fields): 41 millis CompletedMACS2peakCalling pass1 - making usageList (126 chroms): 14 millis pass2 - checking and writing primary data (39580 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:28:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:28:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:28:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101968/ERX101968.20_summits.bed INFO @ Fri, 05 Jul 2019 07:28:39: Done! pass1 - making usageList (71 chroms): 4 millis pass2 - checking and writing primary data (16592 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。