Job ID = 4178409 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-12-05T03:38:27 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 ) 2019-12-05T03:38:27 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 : 26,256,039 reads read : 52,512,078 reads written : 52,512,078 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: 00:17:34 26256039 reads; of these: 26256039 (100.00%) were paired; of these: 11400717 (43.42%) aligned concordantly 0 times 12924424 (49.22%) aligned concordantly exactly 1 time 1930898 (7.35%) aligned concordantly >1 times ---- 11400717 pairs aligned concordantly 0 times; of these: 959427 (8.42%) aligned discordantly 1 time ---- 10441290 pairs aligned 0 times concordantly or discordantly; of these: 20882580 mates make up the pairs; of these: 19824505 (94.93%) aligned 0 times 674571 (3.23%) aligned exactly 1 time 383504 (1.84%) aligned >1 times 62.25% overall alignment rate Time searching: 00:17:35 Overall time: 00:17:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1238171 / 15793938 = 0.0784 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:07:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 05 Dec 2019 13:07:34: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:07:34: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:07:39: 1000000 INFO @ Thu, 05 Dec 2019 13:07:43: 2000000 INFO @ Thu, 05 Dec 2019 13:07:48: 3000000 INFO @ Thu, 05 Dec 2019 13:07:52: 4000000 INFO @ Thu, 05 Dec 2019 13:07:57: 5000000 INFO @ Thu, 05 Dec 2019 13:08:01: 6000000 INFO @ Thu, 05 Dec 2019 13:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 05 Dec 2019 13:08:03: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:08:03: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:08:06: 7000000 INFO @ Thu, 05 Dec 2019 13:08:08: 1000000 INFO @ Thu, 05 Dec 2019 13:08:11: 8000000 INFO @ Thu, 05 Dec 2019 13:08:13: 2000000 INFO @ Thu, 05 Dec 2019 13:08:16: 9000000 INFO @ Thu, 05 Dec 2019 13:08:17: 3000000 INFO @ Thu, 05 Dec 2019 13:08:21: 10000000 INFO @ Thu, 05 Dec 2019 13:08:22: 4000000 INFO @ Thu, 05 Dec 2019 13:08:26: 11000000 INFO @ Thu, 05 Dec 2019 13:08:27: 5000000 INFO @ Thu, 05 Dec 2019 13:08:31: 12000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:08:32: 6000000 INFO @ Thu, 05 Dec 2019 13:08:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 05 Dec 2019 13:08:33: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:08:33: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:08:36: 13000000 INFO @ Thu, 05 Dec 2019 13:08:37: 7000000 INFO @ Thu, 05 Dec 2019 13:08:38: 1000000 INFO @ Thu, 05 Dec 2019 13:08:41: 14000000 INFO @ Thu, 05 Dec 2019 13:08:43: 8000000 INFO @ Thu, 05 Dec 2019 13:08:44: 2000000 INFO @ Thu, 05 Dec 2019 13:08:47: 15000000 INFO @ Thu, 05 Dec 2019 13:08:48: 9000000 INFO @ Thu, 05 Dec 2019 13:08:49: 3000000 INFO @ Thu, 05 Dec 2019 13:08:52: 16000000 INFO @ Thu, 05 Dec 2019 13:08:53: 10000000 INFO @ Thu, 05 Dec 2019 13:08:55: 4000000 INFO @ Thu, 05 Dec 2019 13:08:58: 17000000 INFO @ Thu, 05 Dec 2019 13:08:59: 11000000 INFO @ Thu, 05 Dec 2019 13:09:00: 5000000 INFO @ Thu, 05 Dec 2019 13:09:03: 18000000 INFO @ Thu, 05 Dec 2019 13:09:04: 12000000 INFO @ Thu, 05 Dec 2019 13:09:06: 6000000 INFO @ Thu, 05 Dec 2019 13:09:09: 19000000 INFO @ Thu, 05 Dec 2019 13:09:10: 13000000 INFO @ Thu, 05 Dec 2019 13:09:11: 7000000 INFO @ Thu, 05 Dec 2019 13:09:14: 20000000 INFO @ Thu, 05 Dec 2019 13:09:15: 14000000 INFO @ Thu, 05 Dec 2019 13:09:16: 8000000 INFO @ Thu, 05 Dec 2019 13:09:20: 21000000 INFO @ Thu, 05 Dec 2019 13:09:20: 15000000 INFO @ Thu, 05 Dec 2019 13:09:22: 9000000 INFO @ Thu, 05 Dec 2019 13:09:25: 22000000 INFO @ Thu, 05 Dec 2019 13:09:26: 16000000 INFO @ Thu, 05 Dec 2019 13:09:27: 10000000 INFO @ Thu, 05 Dec 2019 13:09:30: 23000000 INFO @ Thu, 05 Dec 2019 13:09:31: 17000000 INFO @ Thu, 05 Dec 2019 13:09:33: 11000000 INFO @ Thu, 05 Dec 2019 13:09:36: 24000000 INFO @ Thu, 05 Dec 2019 13:09:36: 18000000 INFO @ Thu, 05 Dec 2019 13:09:38: 12000000 INFO @ Thu, 05 Dec 2019 13:09:41: 25000000 INFO @ Thu, 05 Dec 2019 13:09:42: 19000000 INFO @ Thu, 05 Dec 2019 13:09:44: 13000000 INFO @ Thu, 05 Dec 2019 13:09:47: 26000000 INFO @ Thu, 05 Dec 2019 13:09:47: 20000000 INFO @ Thu, 05 Dec 2019 13:09:49: 14000000 INFO @ Thu, 05 Dec 2019 13:09:52: 27000000 INFO @ Thu, 05 Dec 2019 13:09:52: 21000000 INFO @ Thu, 05 Dec 2019 13:09:55: 15000000 INFO @ Thu, 05 Dec 2019 13:09:57: 28000000 INFO @ Thu, 05 Dec 2019 13:09:58: 22000000 INFO @ Thu, 05 Dec 2019 13:10:00: 16000000 INFO @ Thu, 05 Dec 2019 13:10:03: 29000000 INFO @ Thu, 05 Dec 2019 13:10:03: 23000000 INFO @ Thu, 05 Dec 2019 13:10:05: 17000000 INFO @ Thu, 05 Dec 2019 13:10:08: 30000000 INFO @ Thu, 05 Dec 2019 13:10:08: 24000000 INFO @ Thu, 05 Dec 2019 13:10:09: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:10:09: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:10:09: #1 total tags in treatment: 13664935 INFO @ Thu, 05 Dec 2019 13:10:09: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:10:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:10:10: #1 tags after filtering in treatment: 12523902 INFO @ Thu, 05 Dec 2019 13:10:10: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 05 Dec 2019 13:10:10: #1 finished! INFO @ Thu, 05 Dec 2019 13:10:10: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:10:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:10:10: #2 number of paired peaks: 322 WARNING @ Thu, 05 Dec 2019 13:10:10: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Thu, 05 Dec 2019 13:10:10: start model_add_line... INFO @ Thu, 05 Dec 2019 13:10:10: 18000000 INFO @ Thu, 05 Dec 2019 13:10:11: start X-correlation... INFO @ Thu, 05 Dec 2019 13:10:11: end of X-cor INFO @ Thu, 05 Dec 2019 13:10:11: #2 finished! INFO @ Thu, 05 Dec 2019 13:10:11: #2 predicted fragment length is 146 bps INFO @ Thu, 05 Dec 2019 13:10:11: #2 alternative fragment length(s) may be 4,146 bps INFO @ Thu, 05 Dec 2019 13:10:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.05_model.r INFO @ Thu, 05 Dec 2019 13:10:11: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:10:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:10:13: 25000000 INFO @ Thu, 05 Dec 2019 13:10:15: 19000000 INFO @ Thu, 05 Dec 2019 13:10:18: 26000000 INFO @ Thu, 05 Dec 2019 13:10:20: 20000000 INFO @ Thu, 05 Dec 2019 13:10:22: 27000000 INFO @ Thu, 05 Dec 2019 13:10:25: 21000000 INFO @ Thu, 05 Dec 2019 13:10:27: 28000000 INFO @ Thu, 05 Dec 2019 13:10:30: 22000000 INFO @ Thu, 05 Dec 2019 13:10:32: 29000000 INFO @ Thu, 05 Dec 2019 13:10:33: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:10:35: 23000000 INFO @ Thu, 05 Dec 2019 13:10:37: 30000000 INFO @ Thu, 05 Dec 2019 13:10:38: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:10:38: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:10:38: #1 total tags in treatment: 13664935 INFO @ Thu, 05 Dec 2019 13:10:38: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:10:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:10:38: #1 tags after filtering in treatment: 12523902 INFO @ Thu, 05 Dec 2019 13:10:38: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 05 Dec 2019 13:10:38: #1 finished! INFO @ Thu, 05 Dec 2019 13:10:38: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:10:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:10:39: #2 number of paired peaks: 322 WARNING @ Thu, 05 Dec 2019 13:10:39: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Thu, 05 Dec 2019 13:10:39: start model_add_line... INFO @ Thu, 05 Dec 2019 13:10:39: start X-correlation... INFO @ Thu, 05 Dec 2019 13:10:39: end of X-cor INFO @ Thu, 05 Dec 2019 13:10:39: #2 finished! INFO @ Thu, 05 Dec 2019 13:10:39: #2 predicted fragment length is 146 bps INFO @ Thu, 05 Dec 2019 13:10:39: #2 alternative fragment length(s) may be 4,146 bps INFO @ Thu, 05 Dec 2019 13:10:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.10_model.r INFO @ Thu, 05 Dec 2019 13:10:39: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:10:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:10:39: 24000000 INFO @ Thu, 05 Dec 2019 13:10:44: 25000000 INFO @ Thu, 05 Dec 2019 13:10:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:10:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:10:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.05_summits.bed INFO @ Thu, 05 Dec 2019 13:10:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:10:48: 26000000 INFO @ Thu, 05 Dec 2019 13:10:52: 27000000 INFO @ Thu, 05 Dec 2019 13:10:57: 28000000 INFO @ Thu, 05 Dec 2019 13:11:01: 29000000 INFO @ Thu, 05 Dec 2019 13:11:02: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:11:05: 30000000 INFO @ Thu, 05 Dec 2019 13:11:07: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:11:07: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:11:07: #1 total tags in treatment: 13664935 INFO @ Thu, 05 Dec 2019 13:11:07: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:11:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:11:07: #1 tags after filtering in treatment: 12523902 INFO @ Thu, 05 Dec 2019 13:11:07: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 05 Dec 2019 13:11:07: #1 finished! INFO @ Thu, 05 Dec 2019 13:11:07: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:11:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:11:08: #2 number of paired peaks: 322 WARNING @ Thu, 05 Dec 2019 13:11:08: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Thu, 05 Dec 2019 13:11:08: start model_add_line... INFO @ Thu, 05 Dec 2019 13:11:08: start X-correlation... INFO @ Thu, 05 Dec 2019 13:11:08: end of X-cor INFO @ Thu, 05 Dec 2019 13:11:08: #2 finished! INFO @ Thu, 05 Dec 2019 13:11:08: #2 predicted fragment length is 146 bps INFO @ Thu, 05 Dec 2019 13:11:08: #2 alternative fragment length(s) may be 4,146 bps INFO @ Thu, 05 Dec 2019 13:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.20_model.r INFO @ Thu, 05 Dec 2019 13:11:08: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:11:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:11:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:11:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.10_summits.bed INFO @ Thu, 05 Dec 2019 13:11:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (261 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:11:30: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7175088/SRX7175088.20_summits.bed INFO @ Thu, 05 Dec 2019 13:11:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (194 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。