Job ID = 5790644 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T19:55:48 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 : 45,867,093 reads read : 91,734,186 reads written : 45,867,093 reads 0-length : 45,867,093 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:33:17 45867093 reads; of these: 45867093 (100.00%) were unpaired; of these: 5059668 (11.03%) aligned 0 times 37449987 (81.65%) aligned exactly 1 time 3357438 (7.32%) aligned >1 times 88.97% overall alignment rate Time searching: 00:33:20 Overall time: 00:33:20 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 20 files... [bam_rmdupse_core] 21207977 / 40807425 = 0.5197 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 05:53:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.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 05:53:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:53:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:54:06: 1000000 INFO @ Wed, 22 Apr 2020 05:54:12: 2000000 INFO @ Wed, 22 Apr 2020 05:54:18: 3000000 INFO @ Wed, 22 Apr 2020 05:54:25: 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 05:54:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.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 05:54:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:54:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:54:31: 5000000 INFO @ Wed, 22 Apr 2020 05:54:36: 1000000 INFO @ Wed, 22 Apr 2020 05:54:39: 6000000 INFO @ Wed, 22 Apr 2020 05:54:44: 2000000 INFO @ Wed, 22 Apr 2020 05:54:46: 7000000 INFO @ Wed, 22 Apr 2020 05:54:51: 3000000 INFO @ Wed, 22 Apr 2020 05:54:53: 8000000 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 05:54:58: 4000000 INFO @ Wed, 22 Apr 2020 05:54:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.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 05:54:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:54:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:55:00: 9000000 INFO @ Wed, 22 Apr 2020 05:55:06: 5000000 INFO @ Wed, 22 Apr 2020 05:55:08: 1000000 INFO @ Wed, 22 Apr 2020 05:55:08: 10000000 INFO @ Wed, 22 Apr 2020 05:55:14: 6000000 INFO @ Wed, 22 Apr 2020 05:55:16: 11000000 INFO @ Wed, 22 Apr 2020 05:55:17: 2000000 INFO @ Wed, 22 Apr 2020 05:55:22: 7000000 INFO @ Wed, 22 Apr 2020 05:55:24: 12000000 INFO @ Wed, 22 Apr 2020 05:55:25: 3000000 INFO @ Wed, 22 Apr 2020 05:55:29: 8000000 INFO @ Wed, 22 Apr 2020 05:55:32: 13000000 INFO @ Wed, 22 Apr 2020 05:55:34: 4000000 INFO @ Wed, 22 Apr 2020 05:55:37: 9000000 INFO @ Wed, 22 Apr 2020 05:55:40: 14000000 INFO @ Wed, 22 Apr 2020 05:55:42: 5000000 INFO @ Wed, 22 Apr 2020 05:55:45: 10000000 INFO @ Wed, 22 Apr 2020 05:55:48: 15000000 INFO @ Wed, 22 Apr 2020 05:55:51: 6000000 INFO @ Wed, 22 Apr 2020 05:55:53: 11000000 INFO @ Wed, 22 Apr 2020 05:55:56: 16000000 INFO @ Wed, 22 Apr 2020 05:56:00: 7000000 INFO @ Wed, 22 Apr 2020 05:56:01: 12000000 INFO @ Wed, 22 Apr 2020 05:56:04: 17000000 INFO @ Wed, 22 Apr 2020 05:56:08: 8000000 INFO @ Wed, 22 Apr 2020 05:56:09: 13000000 INFO @ Wed, 22 Apr 2020 05:56:11: 18000000 INFO @ Wed, 22 Apr 2020 05:56:17: 14000000 INFO @ Wed, 22 Apr 2020 05:56:17: 9000000 INFO @ Wed, 22 Apr 2020 05:56:19: 19000000 INFO @ Wed, 22 Apr 2020 05:56:24: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:56:24: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:56:24: #1 total tags in treatment: 19599448 INFO @ Wed, 22 Apr 2020 05:56:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:56:24: #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 05:56:24: 15000000 INFO @ Wed, 22 Apr 2020 05:56:25: #1 tags after filtering in treatment: 19599205 INFO @ Wed, 22 Apr 2020 05:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:56:25: #1 finished! INFO @ Wed, 22 Apr 2020 05:56:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:56:25: 10000000 INFO @ Wed, 22 Apr 2020 05:56:27: #2 number of paired peaks: 19077 INFO @ Wed, 22 Apr 2020 05:56:27: start model_add_line... INFO @ Wed, 22 Apr 2020 05:56:27: start X-correlation... INFO @ Wed, 22 Apr 2020 05:56:27: end of X-cor INFO @ Wed, 22 Apr 2020 05:56:27: #2 finished! INFO @ Wed, 22 Apr 2020 05:56:27: #2 predicted fragment length is 172 bps INFO @ Wed, 22 Apr 2020 05:56:27: #2 alternative fragment length(s) may be 172 bps INFO @ Wed, 22 Apr 2020 05:56:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.05_model.r WARNING @ Wed, 22 Apr 2020 05:56:27: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:56:27: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Wed, 22 Apr 2020 05:56:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:56:27: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:56:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:56:32: 16000000 INFO @ Wed, 22 Apr 2020 05:56:34: 11000000 INFO @ Wed, 22 Apr 2020 05:56:40: 17000000 INFO @ Wed, 22 Apr 2020 05:56:42: 12000000 INFO @ Wed, 22 Apr 2020 05:56:48: 18000000 INFO @ Wed, 22 Apr 2020 05:56:51: 13000000 INFO @ Wed, 22 Apr 2020 05:56:55: 19000000 INFO @ Wed, 22 Apr 2020 05:56:59: 14000000 INFO @ Wed, 22 Apr 2020 05:57:00: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:57:00: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:57:00: #1 total tags in treatment: 19599448 INFO @ Wed, 22 Apr 2020 05:57:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:57:00: #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 05:57:00: #1 tags after filtering in treatment: 19599205 INFO @ Wed, 22 Apr 2020 05:57:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:57:00: #1 finished! INFO @ Wed, 22 Apr 2020 05:57:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:57:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:57:02: #2 number of paired peaks: 19077 INFO @ Wed, 22 Apr 2020 05:57:02: start model_add_line... INFO @ Wed, 22 Apr 2020 05:57:03: start X-correlation... INFO @ Wed, 22 Apr 2020 05:57:03: end of X-cor INFO @ Wed, 22 Apr 2020 05:57:03: #2 finished! INFO @ Wed, 22 Apr 2020 05:57:03: #2 predicted fragment length is 172 bps INFO @ Wed, 22 Apr 2020 05:57:03: #2 alternative fragment length(s) may be 172 bps INFO @ Wed, 22 Apr 2020 05:57:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.10_model.r WARNING @ Wed, 22 Apr 2020 05:57:03: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:57:03: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Wed, 22 Apr 2020 05:57:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:57:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:57:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:57:07: 15000000 INFO @ Wed, 22 Apr 2020 05:57:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:57:15: 16000000 INFO @ Wed, 22 Apr 2020 05:57:23: 17000000 INFO @ Wed, 22 Apr 2020 05:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.05_summits.bed INFO @ Wed, 22 Apr 2020 05:57:29: Done! pass1 - making usageList (121 chroms): 3 millis pass2 - checking and writing primary data (23972 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:57:31: 18000000 INFO @ Wed, 22 Apr 2020 05:57:39: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 05:57:43: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:57:43: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:57:43: #1 total tags in treatment: 19599448 INFO @ Wed, 22 Apr 2020 05:57:43: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:57:43: #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 05:57:44: #1 tags after filtering in treatment: 19599205 INFO @ Wed, 22 Apr 2020 05:57:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:57:44: #1 finished! INFO @ Wed, 22 Apr 2020 05:57:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:57:45: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:57:46: #2 number of paired peaks: 19077 INFO @ Wed, 22 Apr 2020 05:57:46: start model_add_line... INFO @ Wed, 22 Apr 2020 05:57:46: start X-correlation... INFO @ Wed, 22 Apr 2020 05:57:46: end of X-cor INFO @ Wed, 22 Apr 2020 05:57:46: #2 finished! INFO @ Wed, 22 Apr 2020 05:57:46: #2 predicted fragment length is 172 bps INFO @ Wed, 22 Apr 2020 05:57:46: #2 alternative fragment length(s) may be 172 bps INFO @ Wed, 22 Apr 2020 05:57:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.20_model.r WARNING @ Wed, 22 Apr 2020 05:57:46: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:57:46: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Wed, 22 Apr 2020 05:57:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:57:46: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:57:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 05:58:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:58:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:58:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.10_summits.bed INFO @ Wed, 22 Apr 2020 05:58:06: Done! pass1 - making usageList (115 chroms): 3 millis pass2 - checking and writing primary data (21764 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:58:29: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:58:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:58:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:58:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299287/SRX5299287.20_summits.bed INFO @ Wed, 22 Apr 2020 05:58:50: Done! pass1 - making usageList (105 chroms): 4 millis pass2 - checking and writing primary data (19669 records, 4 fields): 22 millis CompletedMACS2peakCalling