Job ID = 1300472 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:20:19 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 ) 2019-06-03T10:20:19 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 ) spots read : 22,423,058 reads read : 22,423,058 reads written : 22,423,058 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:06:51 22423058 reads; of these: 22423058 (100.00%) were unpaired; of these: 1224418 (5.46%) aligned 0 times 17850136 (79.61%) aligned exactly 1 time 3348504 (14.93%) aligned >1 times 94.54% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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_sort_core] merging from 12 files... [bam_rmdupse_core] 2232723 / 21198640 = 0.1053 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 @ Mon, 03 Jun 2019 19:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.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 @ Mon, 03 Jun 2019 19:37:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:37:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.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 @ Mon, 03 Jun 2019 19:37:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:37:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.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 @ Mon, 03 Jun 2019 19:37:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:37:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:37:17: 1000000 INFO @ Mon, 03 Jun 2019 19:37:17: 1000000 INFO @ Mon, 03 Jun 2019 19:37:17: 1000000 INFO @ Mon, 03 Jun 2019 19:37:24: 2000000 INFO @ Mon, 03 Jun 2019 19:37:24: 2000000 INFO @ Mon, 03 Jun 2019 19:37:25: 2000000 INFO @ Mon, 03 Jun 2019 19:37:31: 3000000 INFO @ Mon, 03 Jun 2019 19:37:32: 3000000 INFO @ Mon, 03 Jun 2019 19:37:33: 3000000 INFO @ Mon, 03 Jun 2019 19:37:39: 4000000 INFO @ Mon, 03 Jun 2019 19:37:39: 4000000 INFO @ Mon, 03 Jun 2019 19:37:41: 4000000 INFO @ Mon, 03 Jun 2019 19:37:46: 5000000 INFO @ Mon, 03 Jun 2019 19:37:47: 5000000 INFO @ Mon, 03 Jun 2019 19:37:49: 5000000 INFO @ Mon, 03 Jun 2019 19:37:53: 6000000 INFO @ Mon, 03 Jun 2019 19:37:54: 6000000 INFO @ Mon, 03 Jun 2019 19:37:57: 6000000 INFO @ Mon, 03 Jun 2019 19:38:00: 7000000 INFO @ Mon, 03 Jun 2019 19:38:02: 7000000 INFO @ Mon, 03 Jun 2019 19:38:05: 7000000 INFO @ Mon, 03 Jun 2019 19:38:07: 8000000 INFO @ Mon, 03 Jun 2019 19:38:09: 8000000 INFO @ Mon, 03 Jun 2019 19:38:13: 8000000 INFO @ Mon, 03 Jun 2019 19:38:15: 9000000 INFO @ Mon, 03 Jun 2019 19:38:17: 9000000 INFO @ Mon, 03 Jun 2019 19:38:21: 9000000 INFO @ Mon, 03 Jun 2019 19:38:22: 10000000 INFO @ Mon, 03 Jun 2019 19:38:24: 10000000 INFO @ Mon, 03 Jun 2019 19:38:29: 10000000 INFO @ Mon, 03 Jun 2019 19:38:30: 11000000 INFO @ Mon, 03 Jun 2019 19:38:32: 11000000 INFO @ Mon, 03 Jun 2019 19:38:37: 11000000 INFO @ Mon, 03 Jun 2019 19:38:37: 12000000 INFO @ Mon, 03 Jun 2019 19:38:39: 12000000 INFO @ Mon, 03 Jun 2019 19:38:44: 13000000 INFO @ Mon, 03 Jun 2019 19:38:45: 12000000 INFO @ Mon, 03 Jun 2019 19:38:46: 13000000 INFO @ Mon, 03 Jun 2019 19:38:51: 14000000 INFO @ Mon, 03 Jun 2019 19:38:53: 13000000 INFO @ Mon, 03 Jun 2019 19:38:54: 14000000 INFO @ Mon, 03 Jun 2019 19:38:59: 15000000 INFO @ Mon, 03 Jun 2019 19:39:01: 15000000 INFO @ Mon, 03 Jun 2019 19:39:01: 14000000 INFO @ Mon, 03 Jun 2019 19:39:06: 16000000 INFO @ Mon, 03 Jun 2019 19:39:08: 16000000 INFO @ Mon, 03 Jun 2019 19:39:10: 15000000 INFO @ Mon, 03 Jun 2019 19:39:13: 17000000 INFO @ Mon, 03 Jun 2019 19:39:16: 17000000 INFO @ Mon, 03 Jun 2019 19:39:18: 16000000 INFO @ Mon, 03 Jun 2019 19:39:21: 18000000 INFO @ Mon, 03 Jun 2019 19:39:24: 18000000 INFO @ Mon, 03 Jun 2019 19:39:26: 17000000 INFO @ Mon, 03 Jun 2019 19:39:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:39:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:39:28: #1 total tags in treatment: 18965917 INFO @ Mon, 03 Jun 2019 19:39:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:39:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:39:28: #1 tags after filtering in treatment: 18965917 INFO @ Mon, 03 Jun 2019 19:39:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:39:28: #1 finished! INFO @ Mon, 03 Jun 2019 19:39:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:39:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:39:30: #2 number of paired peaks: 245 WARNING @ Mon, 03 Jun 2019 19:39:30: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Mon, 03 Jun 2019 19:39:30: start model_add_line... INFO @ Mon, 03 Jun 2019 19:39:30: start X-correlation... INFO @ Mon, 03 Jun 2019 19:39:30: end of X-cor INFO @ Mon, 03 Jun 2019 19:39:30: #2 finished! INFO @ Mon, 03 Jun 2019 19:39:30: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 19:39:30: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 19:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.10_model.r INFO @ Mon, 03 Jun 2019 19:39:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:39:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:39:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:39:31: #1 total tags in treatment: 18965917 INFO @ Mon, 03 Jun 2019 19:39:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:39:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:39:32: #1 tags after filtering in treatment: 18965917 INFO @ Mon, 03 Jun 2019 19:39:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:39:32: #1 finished! INFO @ Mon, 03 Jun 2019 19:39:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:39:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:39:33: #2 number of paired peaks: 245 WARNING @ Mon, 03 Jun 2019 19:39:33: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Mon, 03 Jun 2019 19:39:33: start model_add_line... INFO @ Mon, 03 Jun 2019 19:39:33: start X-correlation... INFO @ Mon, 03 Jun 2019 19:39:33: end of X-cor INFO @ Mon, 03 Jun 2019 19:39:33: #2 finished! INFO @ Mon, 03 Jun 2019 19:39:33: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 19:39:33: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 19:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.05_model.r INFO @ Mon, 03 Jun 2019 19:39:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:39:35: 18000000 INFO @ Mon, 03 Jun 2019 19:39:43: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:39:43: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:39:43: #1 total tags in treatment: 18965917 INFO @ Mon, 03 Jun 2019 19:39:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:39:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:39:43: #1 tags after filtering in treatment: 18965917 INFO @ Mon, 03 Jun 2019 19:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:39:43: #1 finished! INFO @ Mon, 03 Jun 2019 19:39:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:39:45: #2 number of paired peaks: 245 WARNING @ Mon, 03 Jun 2019 19:39:45: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Mon, 03 Jun 2019 19:39:45: start model_add_line... INFO @ Mon, 03 Jun 2019 19:39:45: start X-correlation... INFO @ Mon, 03 Jun 2019 19:39:45: end of X-cor INFO @ Mon, 03 Jun 2019 19:39:45: #2 finished! INFO @ Mon, 03 Jun 2019 19:39:45: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 19:39:45: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 19:39:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.20_model.r INFO @ Mon, 03 Jun 2019 19:39:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:39:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:40:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:40:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:40:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:40:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:40:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:40:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.10_summits.bed INFO @ Mon, 03 Jun 2019 19:40:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4340 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.05_summits.bed INFO @ Mon, 03 Jun 2019 19:40:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5876 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:41:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:41:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:41:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481130/SRX481130.20_summits.bed INFO @ Mon, 03 Jun 2019 19:41:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2634 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。