Job ID = 5720329 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:24:10 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 : 23,425,507 reads read : 46,851,014 reads written : 23,425,507 reads 0-length : 23,425,507 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:00 23425507 reads; of these: 23425507 (100.00%) were unpaired; of these: 218751 (0.93%) aligned 0 times 20912309 (89.27%) aligned exactly 1 time 2294447 (9.79%) aligned >1 times 99.07% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5066023 / 23206756 = 0.2183 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, 15 Apr 2020 23:44:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 23:44:40: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:44:40: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:44:48: 1000000 INFO @ Wed, 15 Apr 2020 23:44:55: 2000000 INFO @ Wed, 15 Apr 2020 23:45:02: 3000000 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, 15 Apr 2020 23:45:09: 4000000 INFO @ Wed, 15 Apr 2020 23:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 23:45:11: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:45:11: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:45:16: 5000000 INFO @ Wed, 15 Apr 2020 23:45:19: 1000000 INFO @ Wed, 15 Apr 2020 23:45:24: 6000000 INFO @ Wed, 15 Apr 2020 23:45:27: 2000000 INFO @ Wed, 15 Apr 2020 23:45:31: 7000000 INFO @ Wed, 15 Apr 2020 23:45:34: 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, 15 Apr 2020 23:45:39: 8000000 INFO @ Wed, 15 Apr 2020 23:45:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 23:45:41: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:45:41: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:45:42: 4000000 INFO @ Wed, 15 Apr 2020 23:45:47: 9000000 INFO @ Wed, 15 Apr 2020 23:45:49: 1000000 INFO @ Wed, 15 Apr 2020 23:45:50: 5000000 INFO @ Wed, 15 Apr 2020 23:45:54: 10000000 INFO @ Wed, 15 Apr 2020 23:45:56: 2000000 INFO @ Wed, 15 Apr 2020 23:45:57: 6000000 INFO @ Wed, 15 Apr 2020 23:46:02: 11000000 INFO @ Wed, 15 Apr 2020 23:46:04: 3000000 INFO @ Wed, 15 Apr 2020 23:46:05: 7000000 INFO @ Wed, 15 Apr 2020 23:46:09: 12000000 INFO @ Wed, 15 Apr 2020 23:46:11: 4000000 INFO @ Wed, 15 Apr 2020 23:46:13: 8000000 INFO @ Wed, 15 Apr 2020 23:46:17: 13000000 INFO @ Wed, 15 Apr 2020 23:46:19: 5000000 INFO @ Wed, 15 Apr 2020 23:46:21: 9000000 INFO @ Wed, 15 Apr 2020 23:46:25: 14000000 INFO @ Wed, 15 Apr 2020 23:46:27: 6000000 INFO @ Wed, 15 Apr 2020 23:46:29: 10000000 INFO @ Wed, 15 Apr 2020 23:46:32: 15000000 INFO @ Wed, 15 Apr 2020 23:46:35: 7000000 INFO @ Wed, 15 Apr 2020 23:46:36: 11000000 INFO @ Wed, 15 Apr 2020 23:46:40: 16000000 INFO @ Wed, 15 Apr 2020 23:46:43: 8000000 INFO @ Wed, 15 Apr 2020 23:46:44: 12000000 INFO @ Wed, 15 Apr 2020 23:46:48: 17000000 INFO @ Wed, 15 Apr 2020 23:46:51: 9000000 INFO @ Wed, 15 Apr 2020 23:46:52: 13000000 INFO @ Wed, 15 Apr 2020 23:46:55: 18000000 INFO @ Wed, 15 Apr 2020 23:46:56: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:46:56: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:46:56: #1 total tags in treatment: 18140733 INFO @ Wed, 15 Apr 2020 23:46:56: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:46:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:46:57: #1 tags after filtering in treatment: 18140733 INFO @ Wed, 15 Apr 2020 23:46:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:46:57: #1 finished! INFO @ Wed, 15 Apr 2020 23:46:57: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:46:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:46:58: 10000000 INFO @ Wed, 15 Apr 2020 23:46:58: #2 number of paired peaks: 2417 INFO @ Wed, 15 Apr 2020 23:46:58: start model_add_line... INFO @ Wed, 15 Apr 2020 23:46:58: start X-correlation... INFO @ Wed, 15 Apr 2020 23:46:58: end of X-cor INFO @ Wed, 15 Apr 2020 23:46:58: #2 finished! INFO @ Wed, 15 Apr 2020 23:46:58: #2 predicted fragment length is 240 bps INFO @ Wed, 15 Apr 2020 23:46:58: #2 alternative fragment length(s) may be 4,240 bps INFO @ Wed, 15 Apr 2020 23:46:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.05_model.r INFO @ Wed, 15 Apr 2020 23:46:58: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:46:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:47:00: 14000000 INFO @ Wed, 15 Apr 2020 23:47:05: 11000000 INFO @ Wed, 15 Apr 2020 23:47:07: 15000000 INFO @ Wed, 15 Apr 2020 23:47:13: 12000000 INFO @ Wed, 15 Apr 2020 23:47:15: 16000000 INFO @ Wed, 15 Apr 2020 23:47:20: 13000000 INFO @ Wed, 15 Apr 2020 23:47:22: 17000000 INFO @ Wed, 15 Apr 2020 23:47:27: 14000000 INFO @ Wed, 15 Apr 2020 23:47:30: 18000000 INFO @ Wed, 15 Apr 2020 23:47:31: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:47:31: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:47:31: #1 total tags in treatment: 18140733 INFO @ Wed, 15 Apr 2020 23:47:31: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:47:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:47:31: #1 tags after filtering in treatment: 18140733 INFO @ Wed, 15 Apr 2020 23:47:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:47:31: #1 finished! INFO @ Wed, 15 Apr 2020 23:47:31: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:47:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:47:33: #2 number of paired peaks: 2417 INFO @ Wed, 15 Apr 2020 23:47:33: start model_add_line... INFO @ Wed, 15 Apr 2020 23:47:33: start X-correlation... INFO @ Wed, 15 Apr 2020 23:47:33: end of X-cor INFO @ Wed, 15 Apr 2020 23:47:33: #2 finished! INFO @ Wed, 15 Apr 2020 23:47:33: #2 predicted fragment length is 240 bps INFO @ Wed, 15 Apr 2020 23:47:33: #2 alternative fragment length(s) may be 4,240 bps INFO @ Wed, 15 Apr 2020 23:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.10_model.r INFO @ Wed, 15 Apr 2020 23:47:33: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:47:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:47:34: 15000000 INFO @ Wed, 15 Apr 2020 23:47:41: 16000000 INFO @ Wed, 15 Apr 2020 23:47:47: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:47:48: 17000000 INFO @ Wed, 15 Apr 2020 23:47:56: 18000000 INFO @ Wed, 15 Apr 2020 23:47:57: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:47:57: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:47:57: #1 total tags in treatment: 18140733 INFO @ Wed, 15 Apr 2020 23:47:57: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:47:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:47:57: #1 tags after filtering in treatment: 18140733 INFO @ Wed, 15 Apr 2020 23:47:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:47:57: #1 finished! INFO @ Wed, 15 Apr 2020 23:47:57: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:47:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:47:58: #2 number of paired peaks: 2417 INFO @ Wed, 15 Apr 2020 23:47:58: start model_add_line... INFO @ Wed, 15 Apr 2020 23:47:59: start X-correlation... INFO @ Wed, 15 Apr 2020 23:47:59: end of X-cor INFO @ Wed, 15 Apr 2020 23:47:59: #2 finished! INFO @ Wed, 15 Apr 2020 23:47:59: #2 predicted fragment length is 240 bps INFO @ Wed, 15 Apr 2020 23:47:59: #2 alternative fragment length(s) may be 4,240 bps INFO @ Wed, 15 Apr 2020 23:47:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.20_model.r INFO @ Wed, 15 Apr 2020 23:47:59: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:47:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.05_summits.bed INFO @ Wed, 15 Apr 2020 23:48:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (10906 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 15 Apr 2020 23:48:22: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:48:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:48:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:48:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.10_summits.bed INFO @ Wed, 15 Apr 2020 23:48:41: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7757 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:48:48: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971797/SRX7971797.20_summits.bed INFO @ Wed, 15 Apr 2020 23:49:06: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (3985 records, 4 fields): 5 millis CompletedMACS2peakCalling