Job ID = 5720336 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:35:46 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 : 23,156,320 reads read : 46,312,640 reads written : 23,156,320 reads 0-length : 23,156,320 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:04 23156320 reads; of these: 23156320 (100.00%) were unpaired; of these: 1194230 (5.16%) aligned 0 times 18398992 (79.46%) aligned exactly 1 time 3563098 (15.39%) aligned >1 times 94.84% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2252007 / 21962090 = 0.1025 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, 15 Apr 2020 23:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 23:55:48: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:55:48: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:55:57: 1000000 INFO @ Wed, 15 Apr 2020 23:56:05: 2000000 INFO @ Wed, 15 Apr 2020 23:56:14: 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, 15 Apr 2020 23:56:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 23:56:18: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:56:18: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:56:22: 4000000 INFO @ Wed, 15 Apr 2020 23:56:27: 1000000 INFO @ Wed, 15 Apr 2020 23:56:32: 5000000 INFO @ Wed, 15 Apr 2020 23:56:34: 2000000 INFO @ Wed, 15 Apr 2020 23:56:41: 6000000 INFO @ Wed, 15 Apr 2020 23:56:41: 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, 15 Apr 2020 23:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 23:56:48: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:56:48: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:56:49: 4000000 INFO @ Wed, 15 Apr 2020 23:56:50: 7000000 INFO @ Wed, 15 Apr 2020 23:56:55: 1000000 INFO @ Wed, 15 Apr 2020 23:56:57: 5000000 INFO @ Wed, 15 Apr 2020 23:56:59: 8000000 INFO @ Wed, 15 Apr 2020 23:57:02: 2000000 INFO @ Wed, 15 Apr 2020 23:57:05: 6000000 INFO @ Wed, 15 Apr 2020 23:57:08: 9000000 INFO @ Wed, 15 Apr 2020 23:57:08: 3000000 INFO @ Wed, 15 Apr 2020 23:57:13: 7000000 INFO @ Wed, 15 Apr 2020 23:57:15: 4000000 INFO @ Wed, 15 Apr 2020 23:57:17: 10000000 INFO @ Wed, 15 Apr 2020 23:57:21: 8000000 INFO @ Wed, 15 Apr 2020 23:57:22: 5000000 INFO @ Wed, 15 Apr 2020 23:57:26: 11000000 INFO @ Wed, 15 Apr 2020 23:57:29: 6000000 INFO @ Wed, 15 Apr 2020 23:57:29: 9000000 INFO @ Wed, 15 Apr 2020 23:57:35: 7000000 INFO @ Wed, 15 Apr 2020 23:57:35: 12000000 INFO @ Wed, 15 Apr 2020 23:57:37: 10000000 INFO @ Wed, 15 Apr 2020 23:57:42: 8000000 INFO @ Wed, 15 Apr 2020 23:57:44: 11000000 INFO @ Wed, 15 Apr 2020 23:57:45: 13000000 INFO @ Wed, 15 Apr 2020 23:57:49: 9000000 INFO @ Wed, 15 Apr 2020 23:57:52: 12000000 INFO @ Wed, 15 Apr 2020 23:57:54: 14000000 INFO @ Wed, 15 Apr 2020 23:57:56: 10000000 INFO @ Wed, 15 Apr 2020 23:58:00: 13000000 INFO @ Wed, 15 Apr 2020 23:58:02: 11000000 INFO @ Wed, 15 Apr 2020 23:58:03: 15000000 INFO @ Wed, 15 Apr 2020 23:58:07: 14000000 INFO @ Wed, 15 Apr 2020 23:58:09: 12000000 INFO @ Wed, 15 Apr 2020 23:58:12: 16000000 INFO @ Wed, 15 Apr 2020 23:58:15: 15000000 INFO @ Wed, 15 Apr 2020 23:58:16: 13000000 INFO @ Wed, 15 Apr 2020 23:58:21: 17000000 INFO @ Wed, 15 Apr 2020 23:58:22: 16000000 INFO @ Wed, 15 Apr 2020 23:58:23: 14000000 INFO @ Wed, 15 Apr 2020 23:58:29: 15000000 INFO @ Wed, 15 Apr 2020 23:58:30: 17000000 INFO @ Wed, 15 Apr 2020 23:58:30: 18000000 INFO @ Wed, 15 Apr 2020 23:58:36: 16000000 INFO @ Wed, 15 Apr 2020 23:58:37: 18000000 INFO @ Wed, 15 Apr 2020 23:58:39: 19000000 INFO @ Wed, 15 Apr 2020 23:58:43: 17000000 INFO @ Wed, 15 Apr 2020 23:58:45: 19000000 INFO @ Wed, 15 Apr 2020 23:58:45: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:58:45: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:58:45: #1 total tags in treatment: 19710083 INFO @ Wed, 15 Apr 2020 23:58:45: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:58:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:58:46: #1 tags after filtering in treatment: 19710083 INFO @ Wed, 15 Apr 2020 23:58:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:58:46: #1 finished! INFO @ Wed, 15 Apr 2020 23:58:46: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:58:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:58:47: #2 number of paired peaks: 180 WARNING @ Wed, 15 Apr 2020 23:58:47: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Wed, 15 Apr 2020 23:58:47: start model_add_line... INFO @ Wed, 15 Apr 2020 23:58:47: start X-correlation... INFO @ Wed, 15 Apr 2020 23:58:47: end of X-cor INFO @ Wed, 15 Apr 2020 23:58:47: #2 finished! INFO @ Wed, 15 Apr 2020 23:58:47: #2 predicted fragment length is 69 bps INFO @ Wed, 15 Apr 2020 23:58:47: #2 alternative fragment length(s) may be 1,69 bps INFO @ Wed, 15 Apr 2020 23:58:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.05_model.r WARNING @ Wed, 15 Apr 2020 23:58:47: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:58:47: #2 You may need to consider one of the other alternative d(s): 1,69 WARNING @ Wed, 15 Apr 2020 23:58:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:58:47: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:58:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:58:50: 18000000 INFO @ Wed, 15 Apr 2020 23:58:50: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:58:50: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:58:50: #1 total tags in treatment: 19710083 INFO @ Wed, 15 Apr 2020 23:58:50: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:58:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:58:50: #1 tags after filtering in treatment: 19710083 INFO @ Wed, 15 Apr 2020 23:58:50: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:58:50: #1 finished! INFO @ Wed, 15 Apr 2020 23:58:50: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:58:52: #2 number of paired peaks: 180 WARNING @ Wed, 15 Apr 2020 23:58:52: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Wed, 15 Apr 2020 23:58:52: start model_add_line... INFO @ Wed, 15 Apr 2020 23:58:52: start X-correlation... INFO @ Wed, 15 Apr 2020 23:58:52: end of X-cor INFO @ Wed, 15 Apr 2020 23:58:52: #2 finished! INFO @ Wed, 15 Apr 2020 23:58:52: #2 predicted fragment length is 69 bps INFO @ Wed, 15 Apr 2020 23:58:52: #2 alternative fragment length(s) may be 1,69 bps INFO @ Wed, 15 Apr 2020 23:58:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.10_model.r WARNING @ Wed, 15 Apr 2020 23:58:52: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:58:52: #2 You may need to consider one of the other alternative d(s): 1,69 WARNING @ Wed, 15 Apr 2020 23:58:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:58:52: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:58:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:58:56: 19000000 INFO @ Wed, 15 Apr 2020 23:59:00: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:59:00: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:59:00: #1 total tags in treatment: 19710083 INFO @ Wed, 15 Apr 2020 23:59:00: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:59:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:59:01: #1 tags after filtering in treatment: 19710083 INFO @ Wed, 15 Apr 2020 23:59:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:59:01: #1 finished! INFO @ Wed, 15 Apr 2020 23:59:01: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:59:02: #2 number of paired peaks: 180 WARNING @ Wed, 15 Apr 2020 23:59:02: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Wed, 15 Apr 2020 23:59:02: start model_add_line... INFO @ Wed, 15 Apr 2020 23:59:02: start X-correlation... INFO @ Wed, 15 Apr 2020 23:59:02: end of X-cor INFO @ Wed, 15 Apr 2020 23:59:02: #2 finished! INFO @ Wed, 15 Apr 2020 23:59:02: #2 predicted fragment length is 69 bps INFO @ Wed, 15 Apr 2020 23:59:02: #2 alternative fragment length(s) may be 1,69 bps INFO @ Wed, 15 Apr 2020 23:59:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.20_model.r WARNING @ Wed, 15 Apr 2020 23:59:02: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:59:02: #2 You may need to consider one of the other alternative d(s): 1,69 WARNING @ Wed, 15 Apr 2020 23:59:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:59:02: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:59:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:59:19: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:59:24: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:59:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:59:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.05_summits.bed INFO @ Wed, 15 Apr 2020 23:59:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (618 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:59:35: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:59:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:59:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:59:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.10_summits.bed INFO @ Wed, 15 Apr 2020 23:59:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:59:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:59:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:59:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971801/SRX7971801.20_summits.bed INFO @ Wed, 15 Apr 2020 23:59:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (227 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。