Job ID = 5790663 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:28:26 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 ) 2020-04-21T20:28:26 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 ) 2020-04-21T20:28:26 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 : 30,200,147 reads read : 30,200,147 reads written : 30,200,147 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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:08:23 30200147 reads; of these: 30200147 (100.00%) were unpaired; of these: 8496542 (28.13%) aligned 0 times 16855536 (55.81%) aligned exactly 1 time 4848069 (16.05%) aligned >1 times 71.87% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 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] 6981785 / 21703605 = 0.3217 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 05:43:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.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 05:43:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:43:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:43:56: 1000000 INFO @ Wed, 22 Apr 2020 05:44:01: 2000000 INFO @ Wed, 22 Apr 2020 05:44:06: 3000000 INFO @ Wed, 22 Apr 2020 05:44:11: 4000000 INFO @ Wed, 22 Apr 2020 05:44:16: 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 05:44:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.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 05:44:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:44:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:44:21: 6000000 INFO @ Wed, 22 Apr 2020 05:44:26: 1000000 INFO @ Wed, 22 Apr 2020 05:44:26: 7000000 INFO @ Wed, 22 Apr 2020 05:44:31: 2000000 INFO @ Wed, 22 Apr 2020 05:44:32: 8000000 INFO @ Wed, 22 Apr 2020 05:44:37: 3000000 INFO @ Wed, 22 Apr 2020 05:44:37: 9000000 INFO @ Wed, 22 Apr 2020 05:44:42: 4000000 INFO @ Wed, 22 Apr 2020 05:44:43: 10000000 INFO @ Wed, 22 Apr 2020 05:44:47: 5000000 INFO @ Wed, 22 Apr 2020 05:44:48: 11000000 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 05:44:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.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 05:44:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:44:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:44:53: 6000000 INFO @ Wed, 22 Apr 2020 05:44:54: 12000000 INFO @ Wed, 22 Apr 2020 05:44:57: 1000000 INFO @ Wed, 22 Apr 2020 05:44:58: 7000000 INFO @ Wed, 22 Apr 2020 05:44:59: 13000000 INFO @ Wed, 22 Apr 2020 05:45:03: 2000000 INFO @ Wed, 22 Apr 2020 05:45:04: 8000000 INFO @ Wed, 22 Apr 2020 05:45:05: 14000000 INFO @ Wed, 22 Apr 2020 05:45:09: 3000000 INFO @ Wed, 22 Apr 2020 05:45:10: 9000000 INFO @ Wed, 22 Apr 2020 05:45:10: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:45:10: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:45:10: #1 total tags in treatment: 14721820 INFO @ Wed, 22 Apr 2020 05:45:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:45:10: #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 05:45:10: #1 tags after filtering in treatment: 14721620 INFO @ Wed, 22 Apr 2020 05:45:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:45:10: #1 finished! INFO @ Wed, 22 Apr 2020 05:45:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:45:12: #2 number of paired peaks: 32330 INFO @ Wed, 22 Apr 2020 05:45:12: start model_add_line... INFO @ Wed, 22 Apr 2020 05:45:12: start X-correlation... INFO @ Wed, 22 Apr 2020 05:45:12: end of X-cor INFO @ Wed, 22 Apr 2020 05:45:12: #2 finished! INFO @ Wed, 22 Apr 2020 05:45:12: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 05:45:12: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 22 Apr 2020 05:45:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.05_model.r INFO @ Wed, 22 Apr 2020 05:45:12: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:45:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:45:15: 10000000 INFO @ Wed, 22 Apr 2020 05:45:15: 4000000 INFO @ Wed, 22 Apr 2020 05:45:21: 11000000 INFO @ Wed, 22 Apr 2020 05:45:21: 5000000 INFO @ Wed, 22 Apr 2020 05:45:26: 12000000 INFO @ Wed, 22 Apr 2020 05:45:27: 6000000 INFO @ Wed, 22 Apr 2020 05:45:32: 13000000 INFO @ Wed, 22 Apr 2020 05:45:34: 7000000 INFO @ Wed, 22 Apr 2020 05:45:38: 14000000 INFO @ Wed, 22 Apr 2020 05:45:40: 8000000 INFO @ Wed, 22 Apr 2020 05:45:42: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:45:42: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:45:42: #1 total tags in treatment: 14721820 INFO @ Wed, 22 Apr 2020 05:45:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:45:42: #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 05:45:43: #1 tags after filtering in treatment: 14721620 INFO @ Wed, 22 Apr 2020 05:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:45:43: #1 finished! INFO @ Wed, 22 Apr 2020 05:45:43: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:45:45: #2 number of paired peaks: 32330 INFO @ Wed, 22 Apr 2020 05:45:45: start model_add_line... INFO @ Wed, 22 Apr 2020 05:45:45: start X-correlation... INFO @ Wed, 22 Apr 2020 05:45:45: end of X-cor INFO @ Wed, 22 Apr 2020 05:45:45: #2 finished! INFO @ Wed, 22 Apr 2020 05:45:45: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 05:45:45: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 22 Apr 2020 05:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.10_model.r INFO @ Wed, 22 Apr 2020 05:45:45: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:45:46: 9000000 INFO @ Wed, 22 Apr 2020 05:45:49: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:45:52: 10000000 INFO @ Wed, 22 Apr 2020 05:45:58: 11000000 INFO @ Wed, 22 Apr 2020 05:46:04: 12000000 INFO @ Wed, 22 Apr 2020 05:46:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:46:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:46:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.05_summits.bed INFO @ Wed, 22 Apr 2020 05:46:08: Done! pass1 - making usageList (114 chroms): 3 millis pass2 - checking and writing primary data (19271 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:46:10: 13000000 INFO @ Wed, 22 Apr 2020 05:46:16: 14000000 INFO @ Wed, 22 Apr 2020 05:46:20: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:46:20: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:46:20: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:46:20: #1 total tags in treatment: 14721820 INFO @ Wed, 22 Apr 2020 05:46:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:46:20: #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 05:46:21: #1 tags after filtering in treatment: 14721620 INFO @ Wed, 22 Apr 2020 05:46:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:46:21: #1 finished! INFO @ Wed, 22 Apr 2020 05:46:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:46:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:46:23: #2 number of paired peaks: 32330 INFO @ Wed, 22 Apr 2020 05:46:23: start model_add_line... INFO @ Wed, 22 Apr 2020 05:46:23: start X-correlation... INFO @ Wed, 22 Apr 2020 05:46:23: end of X-cor INFO @ Wed, 22 Apr 2020 05:46:23: #2 finished! INFO @ Wed, 22 Apr 2020 05:46:23: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 05:46:23: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 22 Apr 2020 05:46:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.20_model.r INFO @ Wed, 22 Apr 2020 05:46:23: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:46:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:46:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:46:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:46:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.10_summits.bed INFO @ Wed, 22 Apr 2020 05:46:37: Done! pass1 - making usageList (101 chroms): 3 millis pass2 - checking and writing primary data (15076 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:46:57: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 05:47:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:47:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:47:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761699/SRX5761699.20_summits.bed INFO @ Wed, 22 Apr 2020 05:47:15: Done! pass1 - making usageList (81 chroms): 1 millis pass2 - checking and writing primary data (10748 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。