Job ID = 5790797 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T22:31:57 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 : 19,940,207 reads read : 39,880,414 reads written : 19,940,207 reads 0-length : 19,940,207 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: 00:16:04 19940207 reads; of these: 19940207 (100.00%) were unpaired; of these: 564749 (2.83%) aligned 0 times 14260264 (71.52%) aligned exactly 1 time 5115194 (25.65%) aligned >1 times 97.17% overall alignment rate Time searching: 00:16:06 Overall time: 00:16:06 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] 4407022 / 19375458 = 0.2275 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 07:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.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 07:57:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:57:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:57:26: 1000000 INFO @ Wed, 22 Apr 2020 07:57:33: 2000000 INFO @ Wed, 22 Apr 2020 07:57:39: 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 07:57:46: 4000000 INFO @ Wed, 22 Apr 2020 07:57:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.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 07:57:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:57:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:57:52: 5000000 INFO @ Wed, 22 Apr 2020 07:57:56: 1000000 INFO @ Wed, 22 Apr 2020 07:57:59: 6000000 INFO @ Wed, 22 Apr 2020 07:58:02: 2000000 INFO @ Wed, 22 Apr 2020 07:58:06: 7000000 INFO @ Wed, 22 Apr 2020 07:58:09: 3000000 INFO @ Wed, 22 Apr 2020 07:58:13: 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 07:58:16: 4000000 INFO @ Wed, 22 Apr 2020 07:58:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.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 07:58:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:58:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:58:20: 9000000 INFO @ Wed, 22 Apr 2020 07:58:23: 5000000 INFO @ Wed, 22 Apr 2020 07:58:24: 1000000 INFO @ Wed, 22 Apr 2020 07:58:26: 10000000 INFO @ Wed, 22 Apr 2020 07:58:30: 6000000 INFO @ Wed, 22 Apr 2020 07:58:31: 2000000 INFO @ Wed, 22 Apr 2020 07:58:33: 11000000 INFO @ Wed, 22 Apr 2020 07:58:37: 7000000 INFO @ Wed, 22 Apr 2020 07:58:38: 3000000 INFO @ Wed, 22 Apr 2020 07:58:40: 12000000 INFO @ Wed, 22 Apr 2020 07:58:44: 8000000 INFO @ Wed, 22 Apr 2020 07:58:45: 4000000 INFO @ Wed, 22 Apr 2020 07:58:47: 13000000 INFO @ Wed, 22 Apr 2020 07:58:50: 9000000 INFO @ Wed, 22 Apr 2020 07:58:52: 5000000 INFO @ Wed, 22 Apr 2020 07:58:54: 14000000 INFO @ Wed, 22 Apr 2020 07:58:57: 10000000 INFO @ Wed, 22 Apr 2020 07:58:59: 6000000 INFO @ Wed, 22 Apr 2020 07:59:01: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:59:01: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:59:01: #1 total tags in treatment: 14968436 INFO @ Wed, 22 Apr 2020 07:59:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:59:01: #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 07:59:01: #1 tags after filtering in treatment: 14968244 INFO @ Wed, 22 Apr 2020 07:59:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:59:01: #1 finished! INFO @ Wed, 22 Apr 2020 07:59:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:59:03: #2 number of paired peaks: 4125 INFO @ Wed, 22 Apr 2020 07:59:03: start model_add_line... INFO @ Wed, 22 Apr 2020 07:59:03: start X-correlation... INFO @ Wed, 22 Apr 2020 07:59:03: end of X-cor INFO @ Wed, 22 Apr 2020 07:59:03: #2 finished! INFO @ Wed, 22 Apr 2020 07:59:03: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:59:03: #2 alternative fragment length(s) may be 74,586 bps INFO @ Wed, 22 Apr 2020 07:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.05_model.r WARNING @ Wed, 22 Apr 2020 07:59:03: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:59:03: #2 You may need to consider one of the other alternative d(s): 74,586 WARNING @ Wed, 22 Apr 2020 07:59:03: #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 07:59:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:59:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:59:04: 11000000 INFO @ Wed, 22 Apr 2020 07:59:05: 7000000 INFO @ Wed, 22 Apr 2020 07:59:10: 12000000 INFO @ Wed, 22 Apr 2020 07:59:12: 8000000 INFO @ Wed, 22 Apr 2020 07:59:17: 13000000 INFO @ Wed, 22 Apr 2020 07:59:19: 9000000 INFO @ Wed, 22 Apr 2020 07:59:24: 14000000 INFO @ Wed, 22 Apr 2020 07:59:25: 10000000 INFO @ Wed, 22 Apr 2020 07:59:30: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:59:30: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:59:30: #1 total tags in treatment: 14968436 INFO @ Wed, 22 Apr 2020 07:59:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:59:30: #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 07:59:31: #1 tags after filtering in treatment: 14968244 INFO @ Wed, 22 Apr 2020 07:59:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:59:31: #1 finished! INFO @ Wed, 22 Apr 2020 07:59:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:59:32: 11000000 INFO @ Wed, 22 Apr 2020 07:59:32: #2 number of paired peaks: 4125 INFO @ Wed, 22 Apr 2020 07:59:32: start model_add_line... INFO @ Wed, 22 Apr 2020 07:59:32: start X-correlation... INFO @ Wed, 22 Apr 2020 07:59:32: end of X-cor INFO @ Wed, 22 Apr 2020 07:59:32: #2 finished! INFO @ Wed, 22 Apr 2020 07:59:32: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:59:32: #2 alternative fragment length(s) may be 74,586 bps INFO @ Wed, 22 Apr 2020 07:59:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.10_model.r WARNING @ Wed, 22 Apr 2020 07:59:32: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:59:32: #2 You may need to consider one of the other alternative d(s): 74,586 WARNING @ Wed, 22 Apr 2020 07:59:32: #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 07:59:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:59:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:59:39: 12000000 INFO @ Wed, 22 Apr 2020 07:59:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:59:45: 13000000 INFO @ Wed, 22 Apr 2020 07:59:51: 14000000 INFO @ Wed, 22 Apr 2020 07:59:58: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:59:58: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:59:58: #1 total tags in treatment: 14968436 INFO @ Wed, 22 Apr 2020 07:59:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:59:58: #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 07:59:58: #1 tags after filtering in treatment: 14968244 INFO @ Wed, 22 Apr 2020 07:59:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:59:58: #1 finished! INFO @ Wed, 22 Apr 2020 07:59:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:00:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:00: #2 number of paired peaks: 4125 INFO @ Wed, 22 Apr 2020 08:00:00: start model_add_line... INFO @ Wed, 22 Apr 2020 08:00:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.05_summits.bed INFO @ Wed, 22 Apr 2020 08:00:00: Done! INFO @ Wed, 22 Apr 2020 08:00:00: start X-correlation... INFO @ Wed, 22 Apr 2020 08:00:00: end of X-cor INFO @ Wed, 22 Apr 2020 08:00:00: #2 finished! INFO @ Wed, 22 Apr 2020 08:00:00: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 08:00:00: #2 alternative fragment length(s) may be 74,586 bps INFO @ Wed, 22 Apr 2020 08:00:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.20_model.r WARNING @ Wed, 22 Apr 2020 08:00:00: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:00:00: #2 You may need to consider one of the other alternative d(s): 74,586 WARNING @ Wed, 22 Apr 2020 08:00:00: #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 08:00:00: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:00:00: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (857 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:00:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.10_summits.bed INFO @ Wed, 22 Apr 2020 08:00:26: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (531 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:00:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625163/SRX7625163.20_summits.bed INFO @ Wed, 22 Apr 2020 08:00:55: Done! pass1 - making usageList (28 chroms): 0 millis pass2 - checking and writing primary data (315 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。