Job ID = 5790692 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T21:14:14 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 : 34,834,424 reads read : 34,834,424 reads written : 34,834,424 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: 00:07:19 34834424 reads; of these: 34834424 (100.00%) were unpaired; of these: 9146125 (26.26%) aligned 0 times 20802460 (59.72%) aligned exactly 1 time 4885839 (14.03%) aligned >1 times 73.74% overall alignment rate Time searching: 00:07:19 Overall time: 00:07:19 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] 11542740 / 25688299 = 0.4493 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 06:34:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.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 06:34:30: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:34:30: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:34:36: 1000000 INFO @ Wed, 22 Apr 2020 06:34:42: 2000000 INFO @ Wed, 22 Apr 2020 06:34:48: 3000000 INFO @ Wed, 22 Apr 2020 06:34:54: 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 06:35:00: 5000000 INFO @ Wed, 22 Apr 2020 06:35:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.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 06:35:00: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:35:00: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:35:06: 1000000 INFO @ Wed, 22 Apr 2020 06:35:06: 6000000 INFO @ Wed, 22 Apr 2020 06:35:12: 2000000 INFO @ Wed, 22 Apr 2020 06:35:13: 7000000 INFO @ Wed, 22 Apr 2020 06:35:19: 3000000 INFO @ Wed, 22 Apr 2020 06:35:19: 8000000 INFO @ Wed, 22 Apr 2020 06:35:25: 4000000 INFO @ Wed, 22 Apr 2020 06:35:25: 9000000 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 06:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.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 06:35:30: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:35:30: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:35:31: 5000000 INFO @ Wed, 22 Apr 2020 06:35:32: 10000000 INFO @ Wed, 22 Apr 2020 06:35:36: 1000000 INFO @ Wed, 22 Apr 2020 06:35:37: 6000000 INFO @ Wed, 22 Apr 2020 06:35:38: 11000000 INFO @ Wed, 22 Apr 2020 06:35:43: 2000000 INFO @ Wed, 22 Apr 2020 06:35:44: 7000000 INFO @ Wed, 22 Apr 2020 06:35:44: 12000000 INFO @ Wed, 22 Apr 2020 06:35:49: 3000000 INFO @ Wed, 22 Apr 2020 06:35:50: 8000000 INFO @ Wed, 22 Apr 2020 06:35:51: 13000000 INFO @ Wed, 22 Apr 2020 06:35:55: 4000000 INFO @ Wed, 22 Apr 2020 06:35:56: 9000000 INFO @ Wed, 22 Apr 2020 06:35:57: 14000000 INFO @ Wed, 22 Apr 2020 06:35:58: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:35:58: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:35:58: #1 total tags in treatment: 14145559 INFO @ Wed, 22 Apr 2020 06:35:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:35:58: #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 06:35:59: #1 tags after filtering in treatment: 14145350 INFO @ Wed, 22 Apr 2020 06:35:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:35:59: #1 finished! INFO @ Wed, 22 Apr 2020 06:35:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:35:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:36:01: #2 number of paired peaks: 29508 INFO @ Wed, 22 Apr 2020 06:36:01: start model_add_line... INFO @ Wed, 22 Apr 2020 06:36:01: start X-correlation... INFO @ Wed, 22 Apr 2020 06:36:01: end of X-cor INFO @ Wed, 22 Apr 2020 06:36:01: #2 finished! INFO @ Wed, 22 Apr 2020 06:36:01: #2 predicted fragment length is 225 bps INFO @ Wed, 22 Apr 2020 06:36:01: #2 alternative fragment length(s) may be 225 bps INFO @ Wed, 22 Apr 2020 06:36:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.05_model.r INFO @ Wed, 22 Apr 2020 06:36:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:36:01: 5000000 INFO @ Wed, 22 Apr 2020 06:36:03: 10000000 INFO @ Wed, 22 Apr 2020 06:36:08: 6000000 INFO @ Wed, 22 Apr 2020 06:36:09: 11000000 INFO @ Wed, 22 Apr 2020 06:36:14: 7000000 INFO @ Wed, 22 Apr 2020 06:36:15: 12000000 INFO @ Wed, 22 Apr 2020 06:36:20: 8000000 INFO @ Wed, 22 Apr 2020 06:36:22: 13000000 INFO @ Wed, 22 Apr 2020 06:36:26: 9000000 INFO @ Wed, 22 Apr 2020 06:36:28: 14000000 INFO @ Wed, 22 Apr 2020 06:36:29: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:36:29: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:36:29: #1 total tags in treatment: 14145559 INFO @ Wed, 22 Apr 2020 06:36:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:36:29: #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 06:36:29: #1 tags after filtering in treatment: 14145350 INFO @ Wed, 22 Apr 2020 06:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:36:29: #1 finished! INFO @ Wed, 22 Apr 2020 06:36:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:36:31: #2 number of paired peaks: 29508 INFO @ Wed, 22 Apr 2020 06:36:31: start model_add_line... INFO @ Wed, 22 Apr 2020 06:36:32: start X-correlation... INFO @ Wed, 22 Apr 2020 06:36:32: end of X-cor INFO @ Wed, 22 Apr 2020 06:36:32: #2 finished! INFO @ Wed, 22 Apr 2020 06:36:32: #2 predicted fragment length is 225 bps INFO @ Wed, 22 Apr 2020 06:36:32: #2 alternative fragment length(s) may be 225 bps INFO @ Wed, 22 Apr 2020 06:36:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.10_model.r INFO @ Wed, 22 Apr 2020 06:36:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:36:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:36:33: 10000000 INFO @ Wed, 22 Apr 2020 06:36:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:36:39: 11000000 INFO @ Wed, 22 Apr 2020 06:36:46: 12000000 INFO @ Wed, 22 Apr 2020 06:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.05_summits.bed INFO @ Wed, 22 Apr 2020 06:36:50: Done! pass1 - making usageList (127 chroms): 3 millis pass2 - checking and writing primary data (18367 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:36:53: 13000000 INFO @ Wed, 22 Apr 2020 06:37:00: 14000000 INFO @ Wed, 22 Apr 2020 06:37:02: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:37:02: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:37:02: #1 total tags in treatment: 14145559 INFO @ Wed, 22 Apr 2020 06:37:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:37:02: #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 06:37:02: #1 tags after filtering in treatment: 14145350 INFO @ Wed, 22 Apr 2020 06:37:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:37:02: #1 finished! INFO @ Wed, 22 Apr 2020 06:37:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:37:04: #2 number of paired peaks: 29508 INFO @ Wed, 22 Apr 2020 06:37:04: start model_add_line... INFO @ Wed, 22 Apr 2020 06:37:04: start X-correlation... INFO @ Wed, 22 Apr 2020 06:37:04: end of X-cor INFO @ Wed, 22 Apr 2020 06:37:04: #2 finished! INFO @ Wed, 22 Apr 2020 06:37:04: #2 predicted fragment length is 225 bps INFO @ Wed, 22 Apr 2020 06:37:04: #2 alternative fragment length(s) may be 225 bps INFO @ Wed, 22 Apr 2020 06:37:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.20_model.r INFO @ Wed, 22 Apr 2020 06:37:04: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:37:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:37:04: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.10_summits.bed INFO @ Wed, 22 Apr 2020 06:37:22: Done! pass1 - making usageList (104 chroms): 3 millis pass2 - checking and writing primary data (15437 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 06:37:39: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:37:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:37:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:37:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761724/SRX5761724.20_summits.bed INFO @ Wed, 22 Apr 2020 06:37:58: Done! pass1 - making usageList (90 chroms): 2 millis pass2 - checking and writing primary data (12208 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。