Job ID = 5790672 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:55:25 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 : 27,593,551 reads read : 27,593,551 reads written : 27,593,551 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: 00:10:40 27593551 reads; of these: 27593551 (100.00%) were unpaired; of these: 5179476 (18.77%) aligned 0 times 12359509 (44.79%) aligned exactly 1 time 10054566 (36.44%) aligned >1 times 81.23% overall alignment rate Time searching: 00:10:41 Overall time: 00:10:41 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] 2470629 / 22414075 = 0.1102 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 06:19:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.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 06:19:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:19:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:19:30: 1000000 INFO @ Wed, 22 Apr 2020 06:19:35: 2000000 INFO @ Wed, 22 Apr 2020 06:19:41: 3000000 INFO @ Wed, 22 Apr 2020 06:19:47: 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 06:19:53: 5000000 INFO @ Wed, 22 Apr 2020 06:19:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.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 06:19:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:19:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:19:59: 6000000 INFO @ Wed, 22 Apr 2020 06:20:02: 1000000 INFO @ Wed, 22 Apr 2020 06:20:05: 7000000 INFO @ Wed, 22 Apr 2020 06:20:11: 8000000 INFO @ Wed, 22 Apr 2020 06:20:11: 2000000 INFO @ Wed, 22 Apr 2020 06:20:17: 9000000 INFO @ Wed, 22 Apr 2020 06:20:19: 3000000 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 06:20:23: 10000000 INFO @ Wed, 22 Apr 2020 06:20:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.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 06:20:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:20:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:20:27: 4000000 INFO @ Wed, 22 Apr 2020 06:20:29: 11000000 INFO @ Wed, 22 Apr 2020 06:20:31: 1000000 INFO @ Wed, 22 Apr 2020 06:20:35: 12000000 INFO @ Wed, 22 Apr 2020 06:20:36: 5000000 INFO @ Wed, 22 Apr 2020 06:20:38: 2000000 INFO @ Wed, 22 Apr 2020 06:20:41: 13000000 INFO @ Wed, 22 Apr 2020 06:20:44: 3000000 INFO @ Wed, 22 Apr 2020 06:20:45: 6000000 INFO @ Wed, 22 Apr 2020 06:20:46: 14000000 INFO @ Wed, 22 Apr 2020 06:20:51: 4000000 INFO @ Wed, 22 Apr 2020 06:20:52: 15000000 INFO @ Wed, 22 Apr 2020 06:20:53: 7000000 INFO @ Wed, 22 Apr 2020 06:20:57: 5000000 INFO @ Wed, 22 Apr 2020 06:20:58: 16000000 INFO @ Wed, 22 Apr 2020 06:21:01: 8000000 INFO @ Wed, 22 Apr 2020 06:21:03: 6000000 INFO @ Wed, 22 Apr 2020 06:21:04: 17000000 INFO @ Wed, 22 Apr 2020 06:21:09: 9000000 INFO @ Wed, 22 Apr 2020 06:21:10: 7000000 INFO @ Wed, 22 Apr 2020 06:21:10: 18000000 INFO @ Wed, 22 Apr 2020 06:21:16: 8000000 INFO @ Wed, 22 Apr 2020 06:21:17: 19000000 INFO @ Wed, 22 Apr 2020 06:21:17: 10000000 INFO @ Wed, 22 Apr 2020 06:21:22: 9000000 INFO @ Wed, 22 Apr 2020 06:21:22: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:21:22: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:21:22: #1 total tags in treatment: 19943446 INFO @ Wed, 22 Apr 2020 06:21:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:21:22: #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 06:21:23: #1 tags after filtering in treatment: 19943335 INFO @ Wed, 22 Apr 2020 06:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:21:23: #1 finished! INFO @ Wed, 22 Apr 2020 06:21:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:21:25: #2 number of paired peaks: 14803 INFO @ Wed, 22 Apr 2020 06:21:25: start model_add_line... INFO @ Wed, 22 Apr 2020 06:21:25: start X-correlation... INFO @ Wed, 22 Apr 2020 06:21:25: 11000000 INFO @ Wed, 22 Apr 2020 06:21:25: end of X-cor INFO @ Wed, 22 Apr 2020 06:21:25: #2 finished! INFO @ Wed, 22 Apr 2020 06:21:25: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Apr 2020 06:21:25: #2 alternative fragment length(s) may be 41,129 bps INFO @ Wed, 22 Apr 2020 06:21:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.05_model.r INFO @ Wed, 22 Apr 2020 06:21:25: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:21:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:21:28: 10000000 INFO @ Wed, 22 Apr 2020 06:21:33: 12000000 INFO @ Wed, 22 Apr 2020 06:21:34: 11000000 INFO @ Wed, 22 Apr 2020 06:21:40: 12000000 INFO @ Wed, 22 Apr 2020 06:21:40: 13000000 INFO @ Wed, 22 Apr 2020 06:21:46: 13000000 INFO @ Wed, 22 Apr 2020 06:21:48: 14000000 INFO @ Wed, 22 Apr 2020 06:21:52: 14000000 INFO @ Wed, 22 Apr 2020 06:21:54: 15000000 INFO @ Wed, 22 Apr 2020 06:21:58: 15000000 INFO @ Wed, 22 Apr 2020 06:22:00: 16000000 INFO @ Wed, 22 Apr 2020 06:22:04: 16000000 INFO @ Wed, 22 Apr 2020 06:22:06: 17000000 INFO @ Wed, 22 Apr 2020 06:22:10: 17000000 INFO @ Wed, 22 Apr 2020 06:22:11: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:22:12: 18000000 INFO @ Wed, 22 Apr 2020 06:22:16: 18000000 INFO @ Wed, 22 Apr 2020 06:22:18: 19000000 INFO @ Wed, 22 Apr 2020 06:22:22: 19000000 INFO @ Wed, 22 Apr 2020 06:22:24: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:22:24: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:22:24: #1 total tags in treatment: 19943446 INFO @ Wed, 22 Apr 2020 06:22:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:22:24: #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 06:22:25: #1 tags after filtering in treatment: 19943335 INFO @ Wed, 22 Apr 2020 06:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:22:25: #1 finished! INFO @ Wed, 22 Apr 2020 06:22:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:22:27: #2 number of paired peaks: 14803 INFO @ Wed, 22 Apr 2020 06:22:27: start model_add_line... INFO @ Wed, 22 Apr 2020 06:22:27: start X-correlation... INFO @ Wed, 22 Apr 2020 06:22:27: end of X-cor INFO @ Wed, 22 Apr 2020 06:22:27: #2 finished! INFO @ Wed, 22 Apr 2020 06:22:27: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Apr 2020 06:22:27: #2 alternative fragment length(s) may be 41,129 bps INFO @ Wed, 22 Apr 2020 06:22:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.10_model.r INFO @ Wed, 22 Apr 2020 06:22:27: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:22:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:22:28: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:22:28: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:22:28: #1 total tags in treatment: 19943446 INFO @ Wed, 22 Apr 2020 06:22:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:22:28: #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 06:22:29: #1 tags after filtering in treatment: 19943335 INFO @ Wed, 22 Apr 2020 06:22:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:22:29: #1 finished! INFO @ Wed, 22 Apr 2020 06:22:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:22:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:22:31: #2 number of paired peaks: 14803 INFO @ Wed, 22 Apr 2020 06:22:31: start model_add_line... INFO @ Wed, 22 Apr 2020 06:22:31: start X-correlation... INFO @ Wed, 22 Apr 2020 06:22:31: end of X-cor INFO @ Wed, 22 Apr 2020 06:22:31: #2 finished! INFO @ Wed, 22 Apr 2020 06:22:31: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Apr 2020 06:22:31: #2 alternative fragment length(s) may be 41,129 bps INFO @ Wed, 22 Apr 2020 06:22:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.20_model.r INFO @ Wed, 22 Apr 2020 06:22:31: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:22:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:22:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:22:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:22:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.05_summits.bed INFO @ Wed, 22 Apr 2020 06:22:34: Done! pass1 - making usageList (109 chroms): 2 millis pass2 - checking and writing primary data (10099 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:23:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:23:17: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:23:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:23:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:23:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.10_summits.bed INFO @ Wed, 22 Apr 2020 06:23:36: Done! pass1 - making usageList (62 chroms): 0 millis pass2 - checking and writing primary data (1764 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:23:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:23:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:23:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761707/SRX5761707.20_summits.bed INFO @ Wed, 22 Apr 2020 06:23:40: Done! pass1 - making usageList (41 chroms): 0 millis pass2 - checking and writing primary data (564 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。