Job ID = 6368345 SRX = SRX495026 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:21 prefetch.2.10.7: 1) Downloading 'SRR1198558'... 2020-06-16T00:22:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:08 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:08 prefetch.2.10.7: 1) 'SRR1198558' was downloaded successfully Read 24434363 spots for SRR1198558/SRR1198558.sra Written 24434363 spots for SRR1198558/SRR1198558.sra 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: 00:05:23 24434363 reads; of these: 24434363 (100.00%) were unpaired; of these: 3204897 (13.12%) aligned 0 times 17393216 (71.18%) aligned exactly 1 time 3836250 (15.70%) aligned >1 times 86.88% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 2473881 / 21229466 = 0.1165 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 @ Tue, 16 Jun 2020 09:37:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.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 @ Tue, 16 Jun 2020 09:37:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:24: 1000000 INFO @ Tue, 16 Jun 2020 09:37:29: 2000000 INFO @ Tue, 16 Jun 2020 09:37:34: 3000000 INFO @ Tue, 16 Jun 2020 09:37:39: 4000000 INFO @ Tue, 16 Jun 2020 09:37:44: 5000000 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 @ Tue, 16 Jun 2020 09:37:49: 6000000 INFO @ Tue, 16 Jun 2020 09:37:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.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 @ Tue, 16 Jun 2020 09:37:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:54: 7000000 INFO @ Tue, 16 Jun 2020 09:37:54: 1000000 INFO @ Tue, 16 Jun 2020 09:37:59: 8000000 INFO @ Tue, 16 Jun 2020 09:38:00: 2000000 INFO @ Tue, 16 Jun 2020 09:38:04: 9000000 INFO @ Tue, 16 Jun 2020 09:38:05: 3000000 INFO @ Tue, 16 Jun 2020 09:38:09: 10000000 INFO @ Tue, 16 Jun 2020 09:38:10: 4000000 INFO @ Tue, 16 Jun 2020 09:38:15: 11000000 INFO @ Tue, 16 Jun 2020 09:38:15: 5000000 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 @ Tue, 16 Jun 2020 09:38:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.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 @ Tue, 16 Jun 2020 09:38:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:20: 12000000 INFO @ Tue, 16 Jun 2020 09:38:20: 6000000 INFO @ Tue, 16 Jun 2020 09:38:25: 1000000 INFO @ Tue, 16 Jun 2020 09:38:25: 13000000 INFO @ Tue, 16 Jun 2020 09:38:26: 7000000 INFO @ Tue, 16 Jun 2020 09:38:30: 2000000 INFO @ Tue, 16 Jun 2020 09:38:30: 14000000 INFO @ Tue, 16 Jun 2020 09:38:31: 8000000 INFO @ Tue, 16 Jun 2020 09:38:35: 3000000 INFO @ Tue, 16 Jun 2020 09:38:36: 15000000 INFO @ Tue, 16 Jun 2020 09:38:36: 9000000 INFO @ Tue, 16 Jun 2020 09:38:41: 4000000 INFO @ Tue, 16 Jun 2020 09:38:41: 16000000 INFO @ Tue, 16 Jun 2020 09:38:42: 10000000 INFO @ Tue, 16 Jun 2020 09:38:46: 5000000 INFO @ Tue, 16 Jun 2020 09:38:47: 17000000 INFO @ Tue, 16 Jun 2020 09:38:47: 11000000 INFO @ Tue, 16 Jun 2020 09:38:51: 6000000 INFO @ Tue, 16 Jun 2020 09:38:52: 18000000 INFO @ Tue, 16 Jun 2020 09:38:52: 12000000 INFO @ Tue, 16 Jun 2020 09:38:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:38:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:38:56: #1 total tags in treatment: 18755585 INFO @ Tue, 16 Jun 2020 09:38:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:38:56: 7000000 INFO @ Tue, 16 Jun 2020 09:38:56: #1 tags after filtering in treatment: 18755585 INFO @ Tue, 16 Jun 2020 09:38:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:58: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 09:38:58: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:58: 13000000 INFO @ Tue, 16 Jun 2020 09:38:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:58: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 09:38:58: #2 alternative fragment length(s) may be 1,35,45 bps INFO @ Tue, 16 Jun 2020 09:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.05_model.r WARNING @ Tue, 16 Jun 2020 09:38:58: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:38:58: #2 You may need to consider one of the other alternative d(s): 1,35,45 WARNING @ Tue, 16 Jun 2020 09:38:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:38:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:02: 8000000 INFO @ Tue, 16 Jun 2020 09:39:03: 14000000 INFO @ Tue, 16 Jun 2020 09:39:07: 9000000 INFO @ Tue, 16 Jun 2020 09:39:08: 15000000 INFO @ Tue, 16 Jun 2020 09:39:13: 10000000 INFO @ Tue, 16 Jun 2020 09:39:14: 16000000 INFO @ Tue, 16 Jun 2020 09:39:18: 11000000 INFO @ Tue, 16 Jun 2020 09:39:19: 17000000 INFO @ Tue, 16 Jun 2020 09:39:23: 12000000 INFO @ Tue, 16 Jun 2020 09:39:25: 18000000 INFO @ Tue, 16 Jun 2020 09:39:28: 13000000 INFO @ Tue, 16 Jun 2020 09:39:29: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:39:29: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:39:29: #1 total tags in treatment: 18755585 INFO @ Tue, 16 Jun 2020 09:39:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 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 @ Tue, 16 Jun 2020 09:39:29: #1 tags after filtering in treatment: 18755585 INFO @ Tue, 16 Jun 2020 09:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:30: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 09:39:30: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:30: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 09:39:30: #2 alternative fragment length(s) may be 1,35,45 bps INFO @ Tue, 16 Jun 2020 09:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.10_model.r WARNING @ Tue, 16 Jun 2020 09:39:30: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:39:30: #2 You may need to consider one of the other alternative d(s): 1,35,45 WARNING @ Tue, 16 Jun 2020 09:39:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:39:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:34: 14000000 INFO @ Tue, 16 Jun 2020 09:39:39: 15000000 INFO @ Tue, 16 Jun 2020 09:39:44: 16000000 INFO @ Tue, 16 Jun 2020 09:39:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.05_summits.bed INFO @ Tue, 16 Jun 2020 09:39:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (808 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:39:50: 17000000 INFO @ Tue, 16 Jun 2020 09:39:55: 18000000 INFO @ Tue, 16 Jun 2020 09:39:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:39:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:39:59: #1 total tags in treatment: 18755585 INFO @ Tue, 16 Jun 2020 09:39:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:39:59: #1 tags after filtering in treatment: 18755585 INFO @ Tue, 16 Jun 2020 09:39:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:59: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:40:01: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 09:40:01: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:01: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 09:40:01: #2 alternative fragment length(s) may be 1,35,45 bps INFO @ Tue, 16 Jun 2020 09:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.20_model.r WARNING @ Tue, 16 Jun 2020 09:40:01: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:01: #2 You may need to consider one of the other alternative d(s): 1,35,45 WARNING @ Tue, 16 Jun 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 @ Tue, 16 Jun 2020 09:40:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (389 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:40:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495026/SRX495026.20_summits.bed INFO @ Tue, 16 Jun 2020 09:40:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (119 records, 4 fields): 1 millis CompletedMACS2peakCalling