Job ID = 5790687 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T21:05:16 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 : 23,675,187 reads read : 23,675,187 reads written : 23,675,187 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:30 23675187 reads; of these: 23675187 (100.00%) were unpaired; of these: 2394765 (10.12%) aligned 0 times 10507082 (44.38%) aligned exactly 1 time 10773340 (45.50%) aligned >1 times 89.88% overall alignment rate Time searching: 00:10:31 Overall time: 00:10:31 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] 2837492 / 21280422 = 0.1333 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 06:26:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.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 06:26:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:26:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:26:27: 1000000 INFO @ Wed, 22 Apr 2020 06:26:34: 2000000 INFO @ Wed, 22 Apr 2020 06:26:40: 3000000 INFO @ Wed, 22 Apr 2020 06:26:45: 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 06:26:51: 5000000 INFO @ Wed, 22 Apr 2020 06:26:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.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 06:26:51: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:26:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:26:57: 6000000 INFO @ Wed, 22 Apr 2020 06:26:58: 1000000 INFO @ Wed, 22 Apr 2020 06:27:03: 7000000 INFO @ Wed, 22 Apr 2020 06:27:04: 2000000 INFO @ Wed, 22 Apr 2020 06:27:10: 8000000 INFO @ Wed, 22 Apr 2020 06:27:11: 3000000 INFO @ Wed, 22 Apr 2020 06:27:17: 9000000 INFO @ Wed, 22 Apr 2020 06:27:18: 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 06:27:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.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 06:27:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:27:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:27:24: 10000000 INFO @ Wed, 22 Apr 2020 06:27:26: 5000000 INFO @ Wed, 22 Apr 2020 06:27:28: 1000000 INFO @ Wed, 22 Apr 2020 06:27:30: 11000000 INFO @ Wed, 22 Apr 2020 06:27:33: 6000000 INFO @ Wed, 22 Apr 2020 06:27:35: 2000000 INFO @ Wed, 22 Apr 2020 06:27:37: 12000000 INFO @ Wed, 22 Apr 2020 06:27:40: 7000000 INFO @ Wed, 22 Apr 2020 06:27:42: 3000000 INFO @ Wed, 22 Apr 2020 06:27:44: 13000000 INFO @ Wed, 22 Apr 2020 06:27:47: 8000000 INFO @ Wed, 22 Apr 2020 06:27:50: 4000000 INFO @ Wed, 22 Apr 2020 06:27:50: 14000000 INFO @ Wed, 22 Apr 2020 06:27:54: 9000000 INFO @ Wed, 22 Apr 2020 06:27:57: 5000000 INFO @ Wed, 22 Apr 2020 06:27:57: 15000000 INFO @ Wed, 22 Apr 2020 06:28:02: 10000000 INFO @ Wed, 22 Apr 2020 06:28:04: 6000000 INFO @ Wed, 22 Apr 2020 06:28:04: 16000000 INFO @ Wed, 22 Apr 2020 06:28:09: 11000000 INFO @ Wed, 22 Apr 2020 06:28:10: 17000000 INFO @ Wed, 22 Apr 2020 06:28:11: 7000000 INFO @ Wed, 22 Apr 2020 06:28:16: 12000000 INFO @ Wed, 22 Apr 2020 06:28:17: 18000000 INFO @ Wed, 22 Apr 2020 06:28:18: 8000000 INFO @ Wed, 22 Apr 2020 06:28:20: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:28:20: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:28:20: #1 total tags in treatment: 18442930 INFO @ Wed, 22 Apr 2020 06:28:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:28:20: #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 06:28:21: #1 tags after filtering in treatment: 18442820 INFO @ Wed, 22 Apr 2020 06:28:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:28:21: #1 finished! INFO @ Wed, 22 Apr 2020 06:28:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:28:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:28:23: #2 number of paired peaks: 21536 INFO @ Wed, 22 Apr 2020 06:28:23: start model_add_line... INFO @ Wed, 22 Apr 2020 06:28:23: start X-correlation... INFO @ Wed, 22 Apr 2020 06:28:23: end of X-cor INFO @ Wed, 22 Apr 2020 06:28:23: #2 finished! INFO @ Wed, 22 Apr 2020 06:28:23: #2 predicted fragment length is 143 bps INFO @ Wed, 22 Apr 2020 06:28:23: #2 alternative fragment length(s) may be 43,143 bps INFO @ Wed, 22 Apr 2020 06:28:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.05_model.r INFO @ Wed, 22 Apr 2020 06:28:23: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:28:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:28:23: 13000000 INFO @ Wed, 22 Apr 2020 06:28:25: 9000000 INFO @ Wed, 22 Apr 2020 06:28:30: 14000000 INFO @ Wed, 22 Apr 2020 06:28:32: 10000000 INFO @ Wed, 22 Apr 2020 06:28:37: 15000000 INFO @ Wed, 22 Apr 2020 06:28:39: 11000000 INFO @ Wed, 22 Apr 2020 06:28:45: 16000000 INFO @ Wed, 22 Apr 2020 06:28:46: 12000000 INFO @ Wed, 22 Apr 2020 06:28:52: 17000000 INFO @ Wed, 22 Apr 2020 06:28:53: 13000000 INFO @ Wed, 22 Apr 2020 06:28:59: 18000000 INFO @ Wed, 22 Apr 2020 06:29:00: 14000000 INFO @ Wed, 22 Apr 2020 06:29:02: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:29:02: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:29:02: #1 total tags in treatment: 18442930 INFO @ Wed, 22 Apr 2020 06:29:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:29:02: #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 06:29:03: #1 tags after filtering in treatment: 18442820 INFO @ Wed, 22 Apr 2020 06:29:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:29:03: #1 finished! INFO @ Wed, 22 Apr 2020 06:29:03: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:29:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:29:04: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:29:05: #2 number of paired peaks: 21536 INFO @ Wed, 22 Apr 2020 06:29:05: start model_add_line... INFO @ Wed, 22 Apr 2020 06:29:05: start X-correlation... INFO @ Wed, 22 Apr 2020 06:29:05: end of X-cor INFO @ Wed, 22 Apr 2020 06:29:05: #2 finished! INFO @ Wed, 22 Apr 2020 06:29:05: #2 predicted fragment length is 143 bps INFO @ Wed, 22 Apr 2020 06:29:05: #2 alternative fragment length(s) may be 43,143 bps INFO @ Wed, 22 Apr 2020 06:29:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.10_model.r INFO @ Wed, 22 Apr 2020 06:29:05: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:29:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:29:06: 15000000 INFO @ Wed, 22 Apr 2020 06:29:13: 16000000 INFO @ Wed, 22 Apr 2020 06:29:19: 17000000 INFO @ Wed, 22 Apr 2020 06:29:26: 18000000 INFO @ Wed, 22 Apr 2020 06:29:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:29:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:29:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.05_summits.bed INFO @ Wed, 22 Apr 2020 06:29:27: Done! pass1 - making usageList (116 chroms): 2 millis pass2 - checking and writing primary data (10495 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:29:29: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:29:29: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:29:29: #1 total tags in treatment: 18442930 INFO @ Wed, 22 Apr 2020 06:29:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:29:29: #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 06:29:29: #1 tags after filtering in treatment: 18442820 INFO @ Wed, 22 Apr 2020 06:29:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:29:29: #1 finished! INFO @ Wed, 22 Apr 2020 06:29:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:29:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:29:31: #2 number of paired peaks: 21536 INFO @ Wed, 22 Apr 2020 06:29:31: start model_add_line... INFO @ Wed, 22 Apr 2020 06:29:32: start X-correlation... INFO @ Wed, 22 Apr 2020 06:29:32: end of X-cor INFO @ Wed, 22 Apr 2020 06:29:32: #2 finished! INFO @ Wed, 22 Apr 2020 06:29:32: #2 predicted fragment length is 143 bps INFO @ Wed, 22 Apr 2020 06:29:32: #2 alternative fragment length(s) may be 43,143 bps INFO @ Wed, 22 Apr 2020 06:29:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.20_model.r INFO @ Wed, 22 Apr 2020 06:29:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:29:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:29:48: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:30:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:30:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:30:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.10_summits.bed INFO @ Wed, 22 Apr 2020 06:30:09: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (1524 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:30:15: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 06:30:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:30:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:30:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761719/SRX5761719.20_summits.bed INFO @ Wed, 22 Apr 2020 06:30:36: Done! pass1 - making usageList (43 chroms): 0 millis pass2 - checking and writing primary data (610 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。