Job ID = 5721203 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T20:52:36 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 ) spots read : 24,601,095 reads read : 24,601,095 reads written : 24,601,095 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:23 24601095 reads; of these: 24601095 (100.00%) were unpaired; of these: 1100028 (4.47%) aligned 0 times 16440762 (66.83%) aligned exactly 1 time 7060305 (28.70%) aligned >1 times 95.53% overall alignment rate Time searching: 00:08:23 Overall time: 00:08:23 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] 4032765 / 23501067 = 0.1716 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:06:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.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 @ Thu, 16 Apr 2020 06:06:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:06:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:07:02: 1000000 INFO @ Thu, 16 Apr 2020 06:07:06: 2000000 INFO @ Thu, 16 Apr 2020 06:07:11: 3000000 INFO @ Thu, 16 Apr 2020 06:07:16: 4000000 INFO @ Thu, 16 Apr 2020 06:07:21: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:07:25: 6000000 INFO @ Thu, 16 Apr 2020 06:07:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.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 @ Thu, 16 Apr 2020 06:07:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:07:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:07:30: 7000000 INFO @ Thu, 16 Apr 2020 06:07:31: 1000000 INFO @ Thu, 16 Apr 2020 06:07:35: 8000000 INFO @ Thu, 16 Apr 2020 06:07:36: 2000000 INFO @ Thu, 16 Apr 2020 06:07:40: 9000000 INFO @ Thu, 16 Apr 2020 06:07:41: 3000000 INFO @ Thu, 16 Apr 2020 06:07:44: 10000000 INFO @ Thu, 16 Apr 2020 06:07:45: 4000000 INFO @ Thu, 16 Apr 2020 06:07:49: 11000000 INFO @ Thu, 16 Apr 2020 06:07:50: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:07:54: 12000000 INFO @ Thu, 16 Apr 2020 06:07:55: 6000000 INFO @ Thu, 16 Apr 2020 06:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.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 @ Thu, 16 Apr 2020 06:07:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:07:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:07:59: 13000000 INFO @ Thu, 16 Apr 2020 06:08:00: 7000000 INFO @ Thu, 16 Apr 2020 06:08:02: 1000000 INFO @ Thu, 16 Apr 2020 06:08:04: 14000000 INFO @ Thu, 16 Apr 2020 06:08:05: 8000000 INFO @ Thu, 16 Apr 2020 06:08:06: 2000000 INFO @ Thu, 16 Apr 2020 06:08:08: 15000000 INFO @ Thu, 16 Apr 2020 06:08:10: 9000000 INFO @ Thu, 16 Apr 2020 06:08:11: 3000000 INFO @ Thu, 16 Apr 2020 06:08:13: 16000000 INFO @ Thu, 16 Apr 2020 06:08:15: 10000000 INFO @ Thu, 16 Apr 2020 06:08:16: 4000000 INFO @ Thu, 16 Apr 2020 06:08:18: 17000000 INFO @ Thu, 16 Apr 2020 06:08:19: 11000000 INFO @ Thu, 16 Apr 2020 06:08:21: 5000000 INFO @ Thu, 16 Apr 2020 06:08:23: 18000000 INFO @ Thu, 16 Apr 2020 06:08:24: 12000000 INFO @ Thu, 16 Apr 2020 06:08:26: 6000000 INFO @ Thu, 16 Apr 2020 06:08:28: 19000000 INFO @ Thu, 16 Apr 2020 06:08:29: 13000000 INFO @ Thu, 16 Apr 2020 06:08:31: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:08:31: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:08:31: #1 total tags in treatment: 19468302 INFO @ Thu, 16 Apr 2020 06:08:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:08:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:08:31: 7000000 INFO @ Thu, 16 Apr 2020 06:08:31: #1 tags after filtering in treatment: 19468302 INFO @ Thu, 16 Apr 2020 06:08:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:08:31: #1 finished! INFO @ Thu, 16 Apr 2020 06:08:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:08:33: #2 number of paired peaks: 818 WARNING @ Thu, 16 Apr 2020 06:08:33: Fewer paired peaks (818) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 818 pairs to build model! INFO @ Thu, 16 Apr 2020 06:08:33: start model_add_line... INFO @ Thu, 16 Apr 2020 06:08:33: start X-correlation... INFO @ Thu, 16 Apr 2020 06:08:33: end of X-cor INFO @ Thu, 16 Apr 2020 06:08:33: #2 finished! INFO @ Thu, 16 Apr 2020 06:08:33: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 06:08:33: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 06:08:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.05_model.r INFO @ Thu, 16 Apr 2020 06:08:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:08:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:08:34: 14000000 INFO @ Thu, 16 Apr 2020 06:08:36: 8000000 INFO @ Thu, 16 Apr 2020 06:08:39: 15000000 INFO @ Thu, 16 Apr 2020 06:08:41: 9000000 INFO @ Thu, 16 Apr 2020 06:08:44: 16000000 INFO @ Thu, 16 Apr 2020 06:08:45: 10000000 INFO @ Thu, 16 Apr 2020 06:08:48: 17000000 INFO @ Thu, 16 Apr 2020 06:08:50: 11000000 INFO @ Thu, 16 Apr 2020 06:08:53: 18000000 INFO @ Thu, 16 Apr 2020 06:08:55: 12000000 INFO @ Thu, 16 Apr 2020 06:08:58: 19000000 INFO @ Thu, 16 Apr 2020 06:09:00: 13000000 INFO @ Thu, 16 Apr 2020 06:09:01: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:09:01: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:09:01: #1 total tags in treatment: 19468302 INFO @ Thu, 16 Apr 2020 06:09:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:09:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:09:01: #1 tags after filtering in treatment: 19468302 INFO @ Thu, 16 Apr 2020 06:09:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:09:01: #1 finished! INFO @ Thu, 16 Apr 2020 06:09:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:09:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:09:02: #2 number of paired peaks: 818 WARNING @ Thu, 16 Apr 2020 06:09:02: Fewer paired peaks (818) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 818 pairs to build model! INFO @ Thu, 16 Apr 2020 06:09:02: start model_add_line... INFO @ Thu, 16 Apr 2020 06:09:03: start X-correlation... INFO @ Thu, 16 Apr 2020 06:09:03: end of X-cor INFO @ Thu, 16 Apr 2020 06:09:03: #2 finished! INFO @ Thu, 16 Apr 2020 06:09:03: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 06:09:03: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 06:09:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.10_model.r INFO @ Thu, 16 Apr 2020 06:09:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:09:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:09:04: 14000000 INFO @ Thu, 16 Apr 2020 06:09:09: 15000000 INFO @ Thu, 16 Apr 2020 06:09:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:09:14: 16000000 INFO @ Thu, 16 Apr 2020 06:09:18: 17000000 INFO @ Thu, 16 Apr 2020 06:09:23: 18000000 INFO @ Thu, 16 Apr 2020 06:09:28: 19000000 INFO @ Thu, 16 Apr 2020 06:09:30: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:09:30: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:09:30: #1 total tags in treatment: 19468302 INFO @ Thu, 16 Apr 2020 06:09:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:09:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:09:30: #1 tags after filtering in treatment: 19468302 INFO @ Thu, 16 Apr 2020 06:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:09:30: #1 finished! INFO @ Thu, 16 Apr 2020 06:09:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:09:32: #2 number of paired peaks: 818 WARNING @ Thu, 16 Apr 2020 06:09:32: Fewer paired peaks (818) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 818 pairs to build model! INFO @ Thu, 16 Apr 2020 06:09:32: start model_add_line... INFO @ Thu, 16 Apr 2020 06:09:32: start X-correlation... INFO @ Thu, 16 Apr 2020 06:09:32: end of X-cor INFO @ Thu, 16 Apr 2020 06:09:32: #2 finished! INFO @ Thu, 16 Apr 2020 06:09:32: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 06:09:32: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 06:09:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.20_model.r INFO @ Thu, 16 Apr 2020 06:09:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:09:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:09:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:09:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.05_summits.bed INFO @ Thu, 16 Apr 2020 06:09:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7168 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:09:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:10:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:10:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:10:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.10_summits.bed INFO @ Thu, 16 Apr 2020 06:10:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5013 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:10:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827670/SRX6827670.20_summits.bed INFO @ Thu, 16 Apr 2020 06:10:31: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (3226 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。