Job ID = 5790666 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:37:22 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 ) 2020-04-21T20:37:54 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 ) 2020-04-21T20:41:34 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 : 24,863,745 reads read : 24,863,745 reads written : 24,863,745 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: 00:00:03 Time loading forward index: 00:00:06 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:07:02 24863745 reads; of these: 24863745 (100.00%) were unpaired; of these: 4569981 (18.38%) aligned 0 times 15964372 (64.21%) aligned exactly 1 time 4329392 (17.41%) aligned >1 times 81.62% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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] 4565804 / 20293764 = 0.2250 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 05:59:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.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 05:59:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:59:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:59:29: 1000000 INFO @ Wed, 22 Apr 2020 05:59:35: 2000000 INFO @ Wed, 22 Apr 2020 05:59:40: 3000000 INFO @ Wed, 22 Apr 2020 05:59:45: 4000000 INFO @ Wed, 22 Apr 2020 05:59:51: 5000000 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 05:59:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.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 05:59:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:59:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:59:57: 6000000 INFO @ Wed, 22 Apr 2020 06:00:01: 1000000 INFO @ Wed, 22 Apr 2020 06:00:03: 7000000 INFO @ Wed, 22 Apr 2020 06:00:08: 2000000 INFO @ Wed, 22 Apr 2020 06:00:10: 8000000 INFO @ Wed, 22 Apr 2020 06:00:15: 3000000 INFO @ Wed, 22 Apr 2020 06:00:16: 9000000 BedGraph に変換中... INFO @ Wed, 22 Apr 2020 06:00:22: 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 06:00:22: 10000000 INFO @ Wed, 22 Apr 2020 06:00:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.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 06:00:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:00:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:00:29: 11000000 INFO @ Wed, 22 Apr 2020 06:00:29: 5000000 INFO @ Wed, 22 Apr 2020 06:00:31: 1000000 INFO @ Wed, 22 Apr 2020 06:00:36: 12000000 INFO @ Wed, 22 Apr 2020 06:00:36: 6000000 INFO @ Wed, 22 Apr 2020 06:00:38: 2000000 INFO @ Wed, 22 Apr 2020 06:00:42: 13000000 INFO @ Wed, 22 Apr 2020 06:00:44: 7000000 INFO @ Wed, 22 Apr 2020 06:00:44: 3000000 INFO @ Wed, 22 Apr 2020 06:00:49: 14000000 INFO @ Wed, 22 Apr 2020 06:00:51: 8000000 INFO @ Wed, 22 Apr 2020 06:00:51: 4000000 INFO @ Wed, 22 Apr 2020 06:00:56: 15000000 INFO @ Wed, 22 Apr 2020 06:00:58: 9000000 INFO @ Wed, 22 Apr 2020 06:00:58: 5000000 INFO @ Wed, 22 Apr 2020 06:01:01: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:01:01: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:01:01: #1 total tags in treatment: 15727960 INFO @ Wed, 22 Apr 2020 06:01:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:01:01: #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 06:01:01: #1 tags after filtering in treatment: 15727770 INFO @ Wed, 22 Apr 2020 06:01:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:01:01: #1 finished! INFO @ Wed, 22 Apr 2020 06:01:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:01:03: #2 number of paired peaks: 21310 INFO @ Wed, 22 Apr 2020 06:01:03: start model_add_line... INFO @ Wed, 22 Apr 2020 06:01:03: start X-correlation... INFO @ Wed, 22 Apr 2020 06:01:03: end of X-cor INFO @ Wed, 22 Apr 2020 06:01:03: #2 finished! INFO @ Wed, 22 Apr 2020 06:01:03: #2 predicted fragment length is 210 bps INFO @ Wed, 22 Apr 2020 06:01:03: #2 alternative fragment length(s) may be 210 bps INFO @ Wed, 22 Apr 2020 06:01:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.05_model.r INFO @ Wed, 22 Apr 2020 06:01:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:01:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:01:05: 6000000 INFO @ Wed, 22 Apr 2020 06:01:05: 10000000 INFO @ Wed, 22 Apr 2020 06:01:11: 7000000 INFO @ Wed, 22 Apr 2020 06:01:12: 11000000 INFO @ Wed, 22 Apr 2020 06:01:18: 8000000 INFO @ Wed, 22 Apr 2020 06:01:19: 12000000 INFO @ Wed, 22 Apr 2020 06:01:24: 9000000 INFO @ Wed, 22 Apr 2020 06:01:26: 13000000 INFO @ Wed, 22 Apr 2020 06:01:31: 10000000 INFO @ Wed, 22 Apr 2020 06:01:33: 14000000 INFO @ Wed, 22 Apr 2020 06:01:37: 11000000 INFO @ Wed, 22 Apr 2020 06:01:39: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:01:40: 15000000 INFO @ Wed, 22 Apr 2020 06:01:44: 12000000 INFO @ Wed, 22 Apr 2020 06:01:45: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:01:45: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:01:45: #1 total tags in treatment: 15727960 INFO @ Wed, 22 Apr 2020 06:01:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:01:45: #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 06:01:45: #1 tags after filtering in treatment: 15727770 INFO @ Wed, 22 Apr 2020 06:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:01:45: #1 finished! INFO @ Wed, 22 Apr 2020 06:01:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:01:47: #2 number of paired peaks: 21310 INFO @ Wed, 22 Apr 2020 06:01:47: start model_add_line... INFO @ Wed, 22 Apr 2020 06:01:47: start X-correlation... INFO @ Wed, 22 Apr 2020 06:01:47: end of X-cor INFO @ Wed, 22 Apr 2020 06:01:47: #2 finished! INFO @ Wed, 22 Apr 2020 06:01:47: #2 predicted fragment length is 210 bps INFO @ Wed, 22 Apr 2020 06:01:47: #2 alternative fragment length(s) may be 210 bps INFO @ Wed, 22 Apr 2020 06:01:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.10_model.r INFO @ Wed, 22 Apr 2020 06:01:47: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:01:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:01:50: 13000000 INFO @ Wed, 22 Apr 2020 06:01:55: 14000000 INFO @ Wed, 22 Apr 2020 06:01:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:01:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:01:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.05_summits.bed INFO @ Wed, 22 Apr 2020 06:01:58: Done! pass1 - making usageList (129 chroms): 3 millis pass2 - checking and writing primary data (19957 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:02:01: 15000000 INFO @ Wed, 22 Apr 2020 06:02:05: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:02:05: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:02:05: #1 total tags in treatment: 15727960 INFO @ Wed, 22 Apr 2020 06:02:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:02:05: #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 06:02:05: #1 tags after filtering in treatment: 15727770 INFO @ Wed, 22 Apr 2020 06:02:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:02:05: #1 finished! INFO @ Wed, 22 Apr 2020 06:02:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:02:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:02:07: #2 number of paired peaks: 21310 INFO @ Wed, 22 Apr 2020 06:02:07: start model_add_line... INFO @ Wed, 22 Apr 2020 06:02:07: start X-correlation... INFO @ Wed, 22 Apr 2020 06:02:07: end of X-cor INFO @ Wed, 22 Apr 2020 06:02:07: #2 finished! INFO @ Wed, 22 Apr 2020 06:02:07: #2 predicted fragment length is 210 bps INFO @ Wed, 22 Apr 2020 06:02:07: #2 alternative fragment length(s) may be 210 bps INFO @ Wed, 22 Apr 2020 06:02:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.20_model.r INFO @ Wed, 22 Apr 2020 06:02:07: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:02:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:02:24: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:02:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:02:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:02:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.10_summits.bed INFO @ Wed, 22 Apr 2020 06:02:42: Done! pass1 - making usageList (115 chroms): 3 millis pass2 - checking and writing primary data (17218 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:02:45: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:03:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:03:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:03:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761702/SRX5761702.20_summits.bed INFO @ Wed, 22 Apr 2020 06:03:05: Done! pass1 - making usageList (97 chroms): 2 millis pass2 - checking and writing primary data (14762 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。