Job ID = 5790650 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:22:19 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 ) 2020-04-21T20:22:19 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 : 44,041,539 reads read : 88,083,078 reads written : 44,041,539 reads 0-length : 44,041,539 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 04:05:03 44041539 reads; of these: 44041539 (100.00%) were unpaired; of these: 24545269 (55.73%) aligned 0 times 8022867 (18.22%) aligned exactly 1 time 11473403 (26.05%) aligned >1 times 44.27% overall alignment rate Time searching: 04:05:04 Overall time: 04:05:04 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] 3501120 / 19496270 = 0.1796 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 09:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.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 09:36:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:36:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:37:02: 1000000 INFO @ Wed, 22 Apr 2020 09:37:10: 2000000 INFO @ Wed, 22 Apr 2020 09:37:17: 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, 22 Apr 2020 09:37:24: 4000000 INFO @ Wed, 22 Apr 2020 09:37:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.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 09:37:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:37:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:37:32: 5000000 INFO @ Wed, 22 Apr 2020 09:37:33: 1000000 INFO @ Wed, 22 Apr 2020 09:37:40: 6000000 INFO @ Wed, 22 Apr 2020 09:37:41: 2000000 INFO @ Wed, 22 Apr 2020 09:37:47: 7000000 INFO @ Wed, 22 Apr 2020 09:37:49: 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, 22 Apr 2020 09:37:55: 8000000 INFO @ Wed, 22 Apr 2020 09:37:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.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 09:37:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:37:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:37:56: 4000000 INFO @ Wed, 22 Apr 2020 09:38:02: 9000000 INFO @ Wed, 22 Apr 2020 09:38:03: 1000000 INFO @ Wed, 22 Apr 2020 09:38:04: 5000000 INFO @ Wed, 22 Apr 2020 09:38:10: 10000000 INFO @ Wed, 22 Apr 2020 09:38:10: 2000000 INFO @ Wed, 22 Apr 2020 09:38:12: 6000000 INFO @ Wed, 22 Apr 2020 09:38:18: 11000000 INFO @ Wed, 22 Apr 2020 09:38:18: 3000000 INFO @ Wed, 22 Apr 2020 09:38:20: 7000000 INFO @ Wed, 22 Apr 2020 09:38:24: 12000000 INFO @ Wed, 22 Apr 2020 09:38:26: 4000000 INFO @ Wed, 22 Apr 2020 09:38:28: 8000000 INFO @ Wed, 22 Apr 2020 09:38:32: 13000000 INFO @ Wed, 22 Apr 2020 09:38:34: 5000000 INFO @ Wed, 22 Apr 2020 09:38:36: 9000000 INFO @ Wed, 22 Apr 2020 09:38:39: 14000000 INFO @ Wed, 22 Apr 2020 09:38:42: 6000000 INFO @ Wed, 22 Apr 2020 09:38:44: 10000000 INFO @ Wed, 22 Apr 2020 09:38:47: 15000000 INFO @ Wed, 22 Apr 2020 09:38:50: 7000000 INFO @ Wed, 22 Apr 2020 09:38:51: 11000000 INFO @ Wed, 22 Apr 2020 09:38:55: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 09:38:55: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 09:38:55: #1 total tags in treatment: 15995150 INFO @ Wed, 22 Apr 2020 09:38:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:38:55: #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 09:38:55: #1 tags after filtering in treatment: 15995023 INFO @ Wed, 22 Apr 2020 09:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:38:55: #1 finished! INFO @ Wed, 22 Apr 2020 09:38:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:38:57: 8000000 INFO @ Wed, 22 Apr 2020 09:38:58: 12000000 INFO @ Wed, 22 Apr 2020 09:38:59: #2 number of paired peaks: 110233 INFO @ Wed, 22 Apr 2020 09:38:59: start model_add_line... INFO @ Wed, 22 Apr 2020 09:38:59: start X-correlation... INFO @ Wed, 22 Apr 2020 09:38:59: end of X-cor INFO @ Wed, 22 Apr 2020 09:38:59: #2 finished! INFO @ Wed, 22 Apr 2020 09:38:59: #2 predicted fragment length is 107 bps INFO @ Wed, 22 Apr 2020 09:38:59: #2 alternative fragment length(s) may be 107 bps INFO @ Wed, 22 Apr 2020 09:38:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.05_model.r WARNING @ Wed, 22 Apr 2020 09:38:59: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:38:59: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Wed, 22 Apr 2020 09:38:59: #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 09:38:59: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:38:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:39:05: 9000000 INFO @ Wed, 22 Apr 2020 09:39:06: 13000000 INFO @ Wed, 22 Apr 2020 09:39:13: 10000000 INFO @ Wed, 22 Apr 2020 09:39:13: 14000000 INFO @ Wed, 22 Apr 2020 09:39:20: 11000000 INFO @ Wed, 22 Apr 2020 09:39:22: 15000000 INFO @ Wed, 22 Apr 2020 09:39:27: 12000000 INFO @ Wed, 22 Apr 2020 09:39:29: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 09:39:29: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 09:39:29: #1 total tags in treatment: 15995150 INFO @ Wed, 22 Apr 2020 09:39:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:39:29: #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 09:39:30: #1 tags after filtering in treatment: 15995023 INFO @ Wed, 22 Apr 2020 09:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:39:30: #1 finished! INFO @ Wed, 22 Apr 2020 09:39:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:39:34: #2 number of paired peaks: 110233 INFO @ Wed, 22 Apr 2020 09:39:34: start model_add_line... INFO @ Wed, 22 Apr 2020 09:39:34: start X-correlation... INFO @ Wed, 22 Apr 2020 09:39:34: end of X-cor INFO @ Wed, 22 Apr 2020 09:39:34: #2 finished! INFO @ Wed, 22 Apr 2020 09:39:34: #2 predicted fragment length is 107 bps INFO @ Wed, 22 Apr 2020 09:39:34: #2 alternative fragment length(s) may be 107 bps INFO @ Wed, 22 Apr 2020 09:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.10_model.r WARNING @ Wed, 22 Apr 2020 09:39:34: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:39:34: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Wed, 22 Apr 2020 09:39:34: #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 09:39:34: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:39:34: 13000000 INFO @ Wed, 22 Apr 2020 09:39:35: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:39:42: 14000000 INFO @ Wed, 22 Apr 2020 09:39:49: 15000000 INFO @ Wed, 22 Apr 2020 09:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.05_summits.bed INFO @ Wed, 22 Apr 2020 09:39:54: Done! pass1 - making usageList (169 chroms): 6 millis pass2 - checking and writing primary data (44471 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:39:57: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 09:39:57: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 09:39:57: #1 total tags in treatment: 15995150 INFO @ Wed, 22 Apr 2020 09:39:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:39:57: #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 09:39:57: #1 tags after filtering in treatment: 15995023 INFO @ Wed, 22 Apr 2020 09:39:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:39:57: #1 finished! INFO @ Wed, 22 Apr 2020 09:39:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:39:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:40:01: #2 number of paired peaks: 110233 INFO @ Wed, 22 Apr 2020 09:40:01: start model_add_line... INFO @ Wed, 22 Apr 2020 09:40:01: start X-correlation... INFO @ Wed, 22 Apr 2020 09:40:01: end of X-cor INFO @ Wed, 22 Apr 2020 09:40:01: #2 finished! INFO @ Wed, 22 Apr 2020 09:40:01: #2 predicted fragment length is 107 bps INFO @ Wed, 22 Apr 2020 09:40:01: #2 alternative fragment length(s) may be 107 bps INFO @ Wed, 22 Apr 2020 09:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.20_model.r WARNING @ Wed, 22 Apr 2020 09:40:01: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:40:01: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Wed, 22 Apr 2020 09:40:01: #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 09:40:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:40:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:40:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:40:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:40:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.10_summits.bed INFO @ Wed, 22 Apr 2020 09:40:28: Done! pass1 - making usageList (102 chroms): 2 millis pass2 - checking and writing primary data (11108 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:40:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299293/SRX5299293.20_summits.bed INFO @ Wed, 22 Apr 2020 09:40:55: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (1518 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。