Job ID = 5790693 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T21:13:15 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 ) 2020-04-21T21:13:15 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 ) 2020-04-21T21:14:01 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 ) 2020-04-21T21:14:01 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 ) 2020-04-21T21:17:22 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 ) 2020-04-21T21:17:22 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 : 28,148,219 reads read : 28,148,219 reads written : 28,148,219 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: 00:07:13 28148219 reads; of these: 28148219 (100.00%) were unpaired; of these: 6091426 (21.64%) aligned 0 times 17126912 (60.85%) aligned exactly 1 time 4929881 (17.51%) aligned >1 times 78.36% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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] 6335048 / 22056793 = 0.2872 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 @ Wed, 22 Apr 2020 06:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.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 @ Wed, 22 Apr 2020 06:32:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:32:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:32:54: 1000000 INFO @ Wed, 22 Apr 2020 06:32:59: 2000000 INFO @ Wed, 22 Apr 2020 06:33:04: 3000000 INFO @ Wed, 22 Apr 2020 06:33:09: 4000000 INFO @ Wed, 22 Apr 2020 06:33:14: 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 @ Wed, 22 Apr 2020 06:33:19: 6000000 INFO @ Wed, 22 Apr 2020 06:33:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.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 @ Wed, 22 Apr 2020 06:33:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:33:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:33:25: 7000000 INFO @ Wed, 22 Apr 2020 06:33:25: 1000000 INFO @ Wed, 22 Apr 2020 06:33:30: 8000000 INFO @ Wed, 22 Apr 2020 06:33:30: 2000000 INFO @ Wed, 22 Apr 2020 06:33:36: 9000000 INFO @ Wed, 22 Apr 2020 06:33:36: 3000000 INFO @ Wed, 22 Apr 2020 06:33:41: 10000000 INFO @ Wed, 22 Apr 2020 06:33:41: 4000000 INFO @ Wed, 22 Apr 2020 06:33:47: 11000000 INFO @ Wed, 22 Apr 2020 06:33:47: 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 @ Wed, 22 Apr 2020 06:33:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.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 @ Wed, 22 Apr 2020 06:33:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:33:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:33:52: 12000000 INFO @ Wed, 22 Apr 2020 06:33:53: 6000000 INFO @ Wed, 22 Apr 2020 06:33:55: 1000000 INFO @ Wed, 22 Apr 2020 06:33:58: 13000000 INFO @ Wed, 22 Apr 2020 06:33:58: 7000000 INFO @ Wed, 22 Apr 2020 06:34:00: 2000000 INFO @ Wed, 22 Apr 2020 06:34:03: 14000000 INFO @ Wed, 22 Apr 2020 06:34:04: 8000000 INFO @ Wed, 22 Apr 2020 06:34:06: 3000000 INFO @ Wed, 22 Apr 2020 06:34:09: 15000000 INFO @ Wed, 22 Apr 2020 06:34:09: 9000000 INFO @ Wed, 22 Apr 2020 06:34:11: 4000000 INFO @ Wed, 22 Apr 2020 06:34:13: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:34:13: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:34:13: #1 total tags in treatment: 15721745 INFO @ Wed, 22 Apr 2020 06:34:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:34:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:34:13: #1 tags after filtering in treatment: 15721562 INFO @ Wed, 22 Apr 2020 06:34:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:34:13: #1 finished! INFO @ Wed, 22 Apr 2020 06:34:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:34:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:34:15: 10000000 INFO @ Wed, 22 Apr 2020 06:34:16: #2 number of paired peaks: 52599 INFO @ Wed, 22 Apr 2020 06:34:16: start model_add_line... INFO @ Wed, 22 Apr 2020 06:34:16: start X-correlation... INFO @ Wed, 22 Apr 2020 06:34:16: end of X-cor INFO @ Wed, 22 Apr 2020 06:34:16: #2 finished! INFO @ Wed, 22 Apr 2020 06:34:16: #2 predicted fragment length is 230 bps INFO @ Wed, 22 Apr 2020 06:34:16: #2 alternative fragment length(s) may be 230 bps INFO @ Wed, 22 Apr 2020 06:34:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.05_model.r INFO @ Wed, 22 Apr 2020 06:34:16: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:34:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:34:17: 5000000 INFO @ Wed, 22 Apr 2020 06:34:20: 11000000 INFO @ Wed, 22 Apr 2020 06:34:22: 6000000 INFO @ Wed, 22 Apr 2020 06:34:26: 12000000 INFO @ Wed, 22 Apr 2020 06:34:28: 7000000 INFO @ Wed, 22 Apr 2020 06:34:31: 13000000 INFO @ Wed, 22 Apr 2020 06:34:33: 8000000 INFO @ Wed, 22 Apr 2020 06:34:37: 14000000 INFO @ Wed, 22 Apr 2020 06:34:39: 9000000 INFO @ Wed, 22 Apr 2020 06:34:42: 15000000 INFO @ Wed, 22 Apr 2020 06:34:44: 10000000 INFO @ Wed, 22 Apr 2020 06:34:46: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:34:46: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:34:46: #1 total tags in treatment: 15721745 INFO @ Wed, 22 Apr 2020 06:34:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:34:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:34:47: #1 tags after filtering in treatment: 15721562 INFO @ Wed, 22 Apr 2020 06:34:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:34:47: #1 finished! INFO @ Wed, 22 Apr 2020 06:34:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:34:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:34:50: #2 number of paired peaks: 52599 INFO @ Wed, 22 Apr 2020 06:34:50: start model_add_line... INFO @ Wed, 22 Apr 2020 06:34:50: 11000000 INFO @ Wed, 22 Apr 2020 06:34:50: start X-correlation... INFO @ Wed, 22 Apr 2020 06:34:50: end of X-cor INFO @ Wed, 22 Apr 2020 06:34:50: #2 finished! INFO @ Wed, 22 Apr 2020 06:34:50: #2 predicted fragment length is 230 bps INFO @ Wed, 22 Apr 2020 06:34:50: #2 alternative fragment length(s) may be 230 bps INFO @ Wed, 22 Apr 2020 06:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.10_model.r INFO @ Wed, 22 Apr 2020 06:34:50: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:34:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:34:55: 12000000 INFO @ Wed, 22 Apr 2020 06:35:00: 13000000 INFO @ Wed, 22 Apr 2020 06:35:05: 14000000 INFO @ Wed, 22 Apr 2020 06:35:10: 15000000 INFO @ Wed, 22 Apr 2020 06:35:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:35:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:35:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.05_summits.bed INFO @ Wed, 22 Apr 2020 06:35:14: Done! INFO @ Wed, 22 Apr 2020 06:35:14: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:35:14: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:35:14: #1 total tags in treatment: 15721745 INFO @ Wed, 22 Apr 2020 06:35:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:35:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (129 chroms): 3 millis pass2 - checking and writing primary data (21682 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:35:15: #1 tags after filtering in treatment: 15721562 INFO @ Wed, 22 Apr 2020 06:35:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:35:15: #1 finished! INFO @ Wed, 22 Apr 2020 06:35:15: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:35:17: #2 number of paired peaks: 52599 INFO @ Wed, 22 Apr 2020 06:35:17: start model_add_line... INFO @ Wed, 22 Apr 2020 06:35:17: start X-correlation... INFO @ Wed, 22 Apr 2020 06:35:17: end of X-cor INFO @ Wed, 22 Apr 2020 06:35:17: #2 finished! INFO @ Wed, 22 Apr 2020 06:35:17: #2 predicted fragment length is 230 bps INFO @ Wed, 22 Apr 2020 06:35:17: #2 alternative fragment length(s) may be 230 bps INFO @ Wed, 22 Apr 2020 06:35:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.20_model.r INFO @ Wed, 22 Apr 2020 06:35:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:35:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:35:27: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:35:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:35:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:35:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.10_summits.bed INFO @ Wed, 22 Apr 2020 06:35:47: Done! pass1 - making usageList (100 chroms): 3 millis pass2 - checking and writing primary data (15421 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:35:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:36:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:36:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:36:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761725/SRX5761725.20_summits.bed INFO @ Wed, 22 Apr 2020 06:36:13: Done! pass1 - making usageList (73 chroms): 2 millis pass2 - checking and writing primary data (11334 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。