Job ID = 5790808 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T22:35:07 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 ) 2020-04-21T22:35:07 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 : 10,139,776 reads read : 20,279,552 reads written : 10,139,776 reads 0-length : 10,139,776 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: 00:07:09 10139776 reads; of these: 10139776 (100.00%) were unpaired; of these: 289248 (2.85%) aligned 0 times 7357073 (72.56%) aligned exactly 1 time 2493455 (24.59%) aligned >1 times 97.15% overall alignment rate Time searching: 00:07:10 Overall time: 00:07:10 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] 1262979 / 9850528 = 0.1282 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 07:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.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 07:46:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:46:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:47:06: 1000000 INFO @ Wed, 22 Apr 2020 07:47:12: 2000000 INFO @ Wed, 22 Apr 2020 07:47:19: 3000000 INFO @ Wed, 22 Apr 2020 07:47:25: 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 07:47:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.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 07:47:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:47:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:47:32: 5000000 INFO @ Wed, 22 Apr 2020 07:47:37: 1000000 INFO @ Wed, 22 Apr 2020 07:47:39: 6000000 INFO @ Wed, 22 Apr 2020 07:47:45: 2000000 INFO @ Wed, 22 Apr 2020 07:47:47: 7000000 INFO @ Wed, 22 Apr 2020 07:47:52: 3000000 INFO @ Wed, 22 Apr 2020 07:47:55: 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 07:47:59: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:47:59: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:47:59: #1 total tags in treatment: 8587549 INFO @ Wed, 22 Apr 2020 07:47:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:47:59: #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 07:47:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.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 07:47:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:47:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:48:00: #1 tags after filtering in treatment: 8587303 INFO @ Wed, 22 Apr 2020 07:48:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:48:00: #1 finished! INFO @ Wed, 22 Apr 2020 07:48:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:48:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:48:00: 4000000 INFO @ Wed, 22 Apr 2020 07:48:01: #2 number of paired peaks: 5334 INFO @ Wed, 22 Apr 2020 07:48:01: start model_add_line... INFO @ Wed, 22 Apr 2020 07:48:01: start X-correlation... INFO @ Wed, 22 Apr 2020 07:48:01: end of X-cor INFO @ Wed, 22 Apr 2020 07:48:01: #2 finished! INFO @ Wed, 22 Apr 2020 07:48:01: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:48:01: #2 alternative fragment length(s) may be 74 bps INFO @ Wed, 22 Apr 2020 07:48:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.05_model.r WARNING @ Wed, 22 Apr 2020 07:48:01: #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 07:48:01: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Wed, 22 Apr 2020 07:48:01: #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 07:48:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:48:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:48:07: 1000000 INFO @ Wed, 22 Apr 2020 07:48:07: 5000000 INFO @ Wed, 22 Apr 2020 07:48:15: 2000000 INFO @ Wed, 22 Apr 2020 07:48:15: 6000000 INFO @ Wed, 22 Apr 2020 07:48:20: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:48:22: 3000000 INFO @ Wed, 22 Apr 2020 07:48:23: 7000000 INFO @ Wed, 22 Apr 2020 07:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.05_summits.bed INFO @ Wed, 22 Apr 2020 07:48:30: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (598 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:48:30: 4000000 INFO @ Wed, 22 Apr 2020 07:48:30: 8000000 INFO @ Wed, 22 Apr 2020 07:48:35: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:48:35: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:48:35: #1 total tags in treatment: 8587549 INFO @ Wed, 22 Apr 2020 07:48:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:48:35: #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 07:48:35: #1 tags after filtering in treatment: 8587303 INFO @ Wed, 22 Apr 2020 07:48:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:48:35: #1 finished! INFO @ Wed, 22 Apr 2020 07:48:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:48:36: #2 number of paired peaks: 5334 INFO @ Wed, 22 Apr 2020 07:48:36: start model_add_line... INFO @ Wed, 22 Apr 2020 07:48:36: start X-correlation... INFO @ Wed, 22 Apr 2020 07:48:36: end of X-cor INFO @ Wed, 22 Apr 2020 07:48:36: #2 finished! INFO @ Wed, 22 Apr 2020 07:48:36: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:48:36: #2 alternative fragment length(s) may be 74 bps INFO @ Wed, 22 Apr 2020 07:48:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.10_model.r WARNING @ Wed, 22 Apr 2020 07:48:36: #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 07:48:36: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Wed, 22 Apr 2020 07:48:36: #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 07:48:36: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:48:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:48:37: 5000000 INFO @ Wed, 22 Apr 2020 07:48:44: 6000000 INFO @ Wed, 22 Apr 2020 07:48:50: 7000000 INFO @ Wed, 22 Apr 2020 07:48:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:48:57: 8000000 INFO @ Wed, 22 Apr 2020 07:49:00: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:49:00: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:49:00: #1 total tags in treatment: 8587549 INFO @ Wed, 22 Apr 2020 07:49:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:49:00: #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 07:49:01: #1 tags after filtering in treatment: 8587303 INFO @ Wed, 22 Apr 2020 07:49:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:49:01: #1 finished! INFO @ Wed, 22 Apr 2020 07:49:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:49:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:49:02: #2 number of paired peaks: 5334 INFO @ Wed, 22 Apr 2020 07:49:02: start model_add_line... INFO @ Wed, 22 Apr 2020 07:49:02: start X-correlation... INFO @ Wed, 22 Apr 2020 07:49:02: end of X-cor INFO @ Wed, 22 Apr 2020 07:49:02: #2 finished! INFO @ Wed, 22 Apr 2020 07:49:02: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:49:02: #2 alternative fragment length(s) may be 74 bps INFO @ Wed, 22 Apr 2020 07:49:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.20_model.r WARNING @ Wed, 22 Apr 2020 07:49:02: #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 07:49:02: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Wed, 22 Apr 2020 07:49:02: #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 07:49:02: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:49:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.10_summits.bed INFO @ Wed, 22 Apr 2020 07:49:05: Done! pass1 - making usageList (31 chroms): 0 millis pass2 - checking and writing primary data (359 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:49:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625170/SRX7625170.20_summits.bed INFO @ Wed, 22 Apr 2020 07:49:31: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。