Job ID = 5790682 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:58:58 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 : 24,931,868 reads read : 24,931,868 reads written : 24,931,868 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:37 24931868 reads; of these: 24931868 (100.00%) were unpaired; of these: 3412459 (13.69%) aligned 0 times 12722892 (51.03%) aligned exactly 1 time 8796517 (35.28%) aligned >1 times 86.31% overall alignment rate Time searching: 00:08:39 Overall time: 00:08:39 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] 3973159 / 21519409 = 0.1846 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 06:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.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 06:20:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:20:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:20:50: 1000000 INFO @ Wed, 22 Apr 2020 06:20:56: 2000000 INFO @ Wed, 22 Apr 2020 06:21:02: 3000000 INFO @ Wed, 22 Apr 2020 06:21:08: 4000000 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 06:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.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 06:21:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:21:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:21:15: 5000000 INFO @ Wed, 22 Apr 2020 06:21:19: 1000000 INFO @ Wed, 22 Apr 2020 06:21:22: 6000000 INFO @ Wed, 22 Apr 2020 06:21:25: 2000000 INFO @ Wed, 22 Apr 2020 06:21:28: 7000000 INFO @ Wed, 22 Apr 2020 06:21:32: 3000000 INFO @ Wed, 22 Apr 2020 06:21:35: 8000000 INFO @ Wed, 22 Apr 2020 06:21:38: 4000000 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 06:21:41: 9000000 INFO @ Wed, 22 Apr 2020 06:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.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 06:21:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:21:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:21:44: 5000000 INFO @ Wed, 22 Apr 2020 06:21:48: 10000000 INFO @ Wed, 22 Apr 2020 06:21:49: 1000000 INFO @ Wed, 22 Apr 2020 06:21:51: 6000000 INFO @ Wed, 22 Apr 2020 06:21:55: 11000000 INFO @ Wed, 22 Apr 2020 06:21:55: 2000000 INFO @ Wed, 22 Apr 2020 06:21:57: 7000000 INFO @ Wed, 22 Apr 2020 06:22:01: 12000000 INFO @ Wed, 22 Apr 2020 06:22:02: 3000000 INFO @ Wed, 22 Apr 2020 06:22:03: 8000000 INFO @ Wed, 22 Apr 2020 06:22:08: 4000000 INFO @ Wed, 22 Apr 2020 06:22:08: 13000000 INFO @ Wed, 22 Apr 2020 06:22:09: 9000000 INFO @ Wed, 22 Apr 2020 06:22:14: 5000000 INFO @ Wed, 22 Apr 2020 06:22:15: 14000000 INFO @ Wed, 22 Apr 2020 06:22:16: 10000000 INFO @ Wed, 22 Apr 2020 06:22:21: 6000000 INFO @ Wed, 22 Apr 2020 06:22:22: 15000000 INFO @ Wed, 22 Apr 2020 06:22:22: 11000000 INFO @ Wed, 22 Apr 2020 06:22:27: 7000000 INFO @ Wed, 22 Apr 2020 06:22:28: 12000000 INFO @ Wed, 22 Apr 2020 06:22:28: 16000000 INFO @ Wed, 22 Apr 2020 06:22:33: 8000000 INFO @ Wed, 22 Apr 2020 06:22:34: 13000000 INFO @ Wed, 22 Apr 2020 06:22:35: 17000000 INFO @ Wed, 22 Apr 2020 06:22:38: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:22:38: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:22:38: #1 total tags in treatment: 17546250 INFO @ Wed, 22 Apr 2020 06:22:38: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:22:38: #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 06:22:39: #1 tags after filtering in treatment: 17546121 INFO @ Wed, 22 Apr 2020 06:22:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:22:39: #1 finished! INFO @ Wed, 22 Apr 2020 06:22:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:22:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:22:39: 9000000 INFO @ Wed, 22 Apr 2020 06:22:40: 14000000 INFO @ Wed, 22 Apr 2020 06:22:41: #2 number of paired peaks: 27401 INFO @ Wed, 22 Apr 2020 06:22:41: start model_add_line... INFO @ Wed, 22 Apr 2020 06:22:41: start X-correlation... INFO @ Wed, 22 Apr 2020 06:22:41: end of X-cor INFO @ Wed, 22 Apr 2020 06:22:41: #2 finished! INFO @ Wed, 22 Apr 2020 06:22:41: #2 predicted fragment length is 196 bps INFO @ Wed, 22 Apr 2020 06:22:41: #2 alternative fragment length(s) may be 196 bps INFO @ Wed, 22 Apr 2020 06:22:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.05_model.r INFO @ Wed, 22 Apr 2020 06:22:41: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:22:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:22:45: 10000000 INFO @ Wed, 22 Apr 2020 06:22:46: 15000000 INFO @ Wed, 22 Apr 2020 06:22:51: 11000000 INFO @ Wed, 22 Apr 2020 06:22:52: 16000000 INFO @ Wed, 22 Apr 2020 06:22:57: 12000000 INFO @ Wed, 22 Apr 2020 06:22:58: 17000000 INFO @ Wed, 22 Apr 2020 06:23:01: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:23:01: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:23:01: #1 total tags in treatment: 17546250 INFO @ Wed, 22 Apr 2020 06:23:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:23:01: #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 06:23:01: #1 tags after filtering in treatment: 17546121 INFO @ Wed, 22 Apr 2020 06:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:23:01: #1 finished! INFO @ Wed, 22 Apr 2020 06:23:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:23:02: 13000000 INFO @ Wed, 22 Apr 2020 06:23:04: #2 number of paired peaks: 27401 INFO @ Wed, 22 Apr 2020 06:23:04: start model_add_line... INFO @ Wed, 22 Apr 2020 06:23:04: start X-correlation... INFO @ Wed, 22 Apr 2020 06:23:04: end of X-cor INFO @ Wed, 22 Apr 2020 06:23:04: #2 finished! INFO @ Wed, 22 Apr 2020 06:23:04: #2 predicted fragment length is 196 bps INFO @ Wed, 22 Apr 2020 06:23:04: #2 alternative fragment length(s) may be 196 bps INFO @ Wed, 22 Apr 2020 06:23:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.10_model.r INFO @ Wed, 22 Apr 2020 06:23:04: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:23:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:23:08: 14000000 INFO @ Wed, 22 Apr 2020 06:23:13: 15000000 INFO @ Wed, 22 Apr 2020 06:23:19: 16000000 INFO @ Wed, 22 Apr 2020 06:23:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:23:24: 17000000 INFO @ Wed, 22 Apr 2020 06:23:27: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:23:27: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:23:27: #1 total tags in treatment: 17546250 INFO @ Wed, 22 Apr 2020 06:23:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:23:27: #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 06:23:27: #1 tags after filtering in treatment: 17546121 INFO @ Wed, 22 Apr 2020 06:23:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:23:27: #1 finished! INFO @ Wed, 22 Apr 2020 06:23:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:23:29: #2 number of paired peaks: 27401 INFO @ Wed, 22 Apr 2020 06:23:29: start model_add_line... INFO @ Wed, 22 Apr 2020 06:23:30: start X-correlation... INFO @ Wed, 22 Apr 2020 06:23:30: end of X-cor INFO @ Wed, 22 Apr 2020 06:23:30: #2 finished! INFO @ Wed, 22 Apr 2020 06:23:30: #2 predicted fragment length is 196 bps INFO @ Wed, 22 Apr 2020 06:23:30: #2 alternative fragment length(s) may be 196 bps INFO @ Wed, 22 Apr 2020 06:23:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.20_model.r INFO @ Wed, 22 Apr 2020 06:23:30: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:23:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:23:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:23:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:23:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.05_summits.bed INFO @ Wed, 22 Apr 2020 06:23:42: Done! pass1 - making usageList (110 chroms): 2 millis pass2 - checking and writing primary data (8883 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:23:43: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:24:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:24:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.10_summits.bed INFO @ Wed, 22 Apr 2020 06:24:04: Done! pass1 - making usageList (81 chroms): 4 millis pass2 - checking and writing primary data (5185 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:24:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:24:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:24:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:24:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761715/SRX5761715.20_summits.bed INFO @ Wed, 22 Apr 2020 06:24:32: Done! pass1 - making usageList (62 chroms): 0 millis pass2 - checking and writing primary data (2528 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。