Job ID = 5790688 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T21:03:41 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 ) 2020-04-21T21:03:52 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 ) 2020-04-21T21:03:52 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 ) 2020-04-21T21:03:52 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 ) 2020-04-21T21:04:45 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 ) 2020-04-21T21:06:31 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 : 17,562,104 reads read : 17,562,104 reads written : 17,562,104 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: 00:06:33 17562104 reads; of these: 17562104 (100.00%) were unpaired; of these: 2524721 (14.38%) aligned 0 times 7825367 (44.56%) aligned exactly 1 time 7212016 (41.07%) aligned >1 times 85.62% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 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_rmdupse_core] 1756465 / 15037383 = 0.1168 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 06:21:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.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 06:21:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:21:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:21:35: 1000000 INFO @ Wed, 22 Apr 2020 06:21:40: 2000000 INFO @ Wed, 22 Apr 2020 06:21:45: 3000000 INFO @ Wed, 22 Apr 2020 06:21:50: 4000000 INFO @ Wed, 22 Apr 2020 06:21:56: 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 06:22:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.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 06:22:00: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:22:00: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:22:01: 6000000 INFO @ Wed, 22 Apr 2020 06:22:06: 1000000 INFO @ Wed, 22 Apr 2020 06:22:07: 7000000 INFO @ Wed, 22 Apr 2020 06:22:12: 2000000 INFO @ Wed, 22 Apr 2020 06:22:13: 8000000 INFO @ Wed, 22 Apr 2020 06:22:18: 3000000 INFO @ Wed, 22 Apr 2020 06:22:19: 9000000 INFO @ Wed, 22 Apr 2020 06:22:23: 4000000 INFO @ Wed, 22 Apr 2020 06:22:24: 10000000 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 06:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.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 06:22:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:22:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:22:29: 5000000 INFO @ Wed, 22 Apr 2020 06:22:30: 11000000 INFO @ Wed, 22 Apr 2020 06:22:36: 1000000 INFO @ Wed, 22 Apr 2020 06:22:36: 6000000 INFO @ Wed, 22 Apr 2020 06:22:37: 12000000 INFO @ Wed, 22 Apr 2020 06:22:42: 7000000 INFO @ Wed, 22 Apr 2020 06:22:42: 2000000 INFO @ Wed, 22 Apr 2020 06:22:43: 13000000 INFO @ Wed, 22 Apr 2020 06:22:45: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:22:45: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:22:45: #1 total tags in treatment: 13280918 INFO @ Wed, 22 Apr 2020 06:22:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:22:45: #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 06:22:45: #1 tags after filtering in treatment: 13280790 INFO @ Wed, 22 Apr 2020 06:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:22:45: #1 finished! INFO @ Wed, 22 Apr 2020 06:22:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:22:47: #2 number of paired peaks: 17348 INFO @ Wed, 22 Apr 2020 06:22:47: start model_add_line... INFO @ Wed, 22 Apr 2020 06:22:47: start X-correlation... INFO @ Wed, 22 Apr 2020 06:22:47: end of X-cor INFO @ Wed, 22 Apr 2020 06:22:47: #2 finished! INFO @ Wed, 22 Apr 2020 06:22:47: #2 predicted fragment length is 196 bps INFO @ Wed, 22 Apr 2020 06:22:47: #2 alternative fragment length(s) may be 40,196 bps INFO @ Wed, 22 Apr 2020 06:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.05_model.r INFO @ Wed, 22 Apr 2020 06:22:47: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:22:48: 8000000 INFO @ Wed, 22 Apr 2020 06:22:49: 3000000 INFO @ Wed, 22 Apr 2020 06:22:54: 9000000 INFO @ Wed, 22 Apr 2020 06:22:55: 4000000 INFO @ Wed, 22 Apr 2020 06:23:01: 10000000 INFO @ Wed, 22 Apr 2020 06:23:01: 5000000 INFO @ Wed, 22 Apr 2020 06:23:07: 11000000 INFO @ Wed, 22 Apr 2020 06:23:07: 6000000 INFO @ Wed, 22 Apr 2020 06:23:13: 12000000 INFO @ Wed, 22 Apr 2020 06:23:13: 7000000 INFO @ Wed, 22 Apr 2020 06:23:18: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:23:19: 13000000 INFO @ Wed, 22 Apr 2020 06:23:19: 8000000 INFO @ Wed, 22 Apr 2020 06:23:21: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:23:21: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:23:21: #1 total tags in treatment: 13280918 INFO @ Wed, 22 Apr 2020 06:23:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:23:21: #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 06:23:21: #1 tags after filtering in treatment: 13280790 INFO @ Wed, 22 Apr 2020 06:23:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:23:21: #1 finished! INFO @ Wed, 22 Apr 2020 06:23:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:23:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:23:23: #2 number of paired peaks: 17348 INFO @ Wed, 22 Apr 2020 06:23:23: start model_add_line... INFO @ Wed, 22 Apr 2020 06:23:23: start X-correlation... INFO @ Wed, 22 Apr 2020 06:23:23: end of X-cor INFO @ Wed, 22 Apr 2020 06:23:23: #2 finished! INFO @ Wed, 22 Apr 2020 06:23:23: #2 predicted fragment length is 196 bps INFO @ Wed, 22 Apr 2020 06:23:23: #2 alternative fragment length(s) may be 40,196 bps INFO @ Wed, 22 Apr 2020 06:23:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.10_model.r INFO @ Wed, 22 Apr 2020 06:23:23: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:23:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:23:25: 9000000 INFO @ Wed, 22 Apr 2020 06:23:30: 10000000 INFO @ Wed, 22 Apr 2020 06:23:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:23:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:23:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.05_summits.bed INFO @ Wed, 22 Apr 2020 06:23:33: Done! INFO @ Wed, 22 Apr 2020 06:23:35: 11000000 pass1 - making usageList (83 chroms): 2 millis pass2 - checking and writing primary data (5408 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:23:41: 12000000 INFO @ Wed, 22 Apr 2020 06:23:46: 13000000 INFO @ Wed, 22 Apr 2020 06:23:48: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:23:48: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:23:48: #1 total tags in treatment: 13280918 INFO @ Wed, 22 Apr 2020 06:23:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:23:48: #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 06:23:48: #1 tags after filtering in treatment: 13280790 INFO @ Wed, 22 Apr 2020 06:23:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:23:48: #1 finished! INFO @ Wed, 22 Apr 2020 06:23:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:23:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:23:50: #2 number of paired peaks: 17348 INFO @ Wed, 22 Apr 2020 06:23:50: start model_add_line... INFO @ Wed, 22 Apr 2020 06:23:50: start X-correlation... INFO @ Wed, 22 Apr 2020 06:23:50: end of X-cor INFO @ Wed, 22 Apr 2020 06:23:50: #2 finished! INFO @ Wed, 22 Apr 2020 06:23:50: #2 predicted fragment length is 196 bps INFO @ Wed, 22 Apr 2020 06:23:50: #2 alternative fragment length(s) may be 40,196 bps INFO @ Wed, 22 Apr 2020 06:23:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.20_model.r INFO @ Wed, 22 Apr 2020 06:23:50: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:23:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:23:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:24:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:24:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.10_summits.bed INFO @ Wed, 22 Apr 2020 06:24:08: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (1089 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:24:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 06:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761720/SRX5761720.20_summits.bed INFO @ Wed, 22 Apr 2020 06:24:37: Done! pass1 - making usageList (36 chroms): 0 millis pass2 - checking and writing primary data (431 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。