Job ID = 6367010 SRX = SRX257708 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:46 prefetch.2.10.7: 1) Downloading 'SRR800728'... 2020-06-15T23:10:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:47 prefetch.2.10.7: 1) 'SRR800728' was downloaded successfully Read 28372619 spots for SRR800728/SRR800728.sra Written 28372619 spots for SRR800728/SRR800728.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: 00:06:22 28372619 reads; of these: 28372619 (100.00%) were unpaired; of these: 78016 (0.27%) aligned 0 times 23642460 (83.33%) aligned exactly 1 time 4652143 (16.40%) aligned >1 times 99.73% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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] 4182989 / 28294603 = 0.1478 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 08:28:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.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 08:28:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:39: 1000000 INFO @ Tue, 16 Jun 2020 08:28:44: 2000000 INFO @ Tue, 16 Jun 2020 08:28:49: 3000000 INFO @ Tue, 16 Jun 2020 08:28:55: 4000000 INFO @ Tue, 16 Jun 2020 08:29:00: 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 08:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.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 08:29:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:06: 6000000 INFO @ Tue, 16 Jun 2020 08:29:09: 1000000 INFO @ Tue, 16 Jun 2020 08:29:11: 7000000 INFO @ Tue, 16 Jun 2020 08:29:15: 2000000 INFO @ Tue, 16 Jun 2020 08:29:17: 8000000 INFO @ Tue, 16 Jun 2020 08:29:21: 3000000 INFO @ Tue, 16 Jun 2020 08:29:23: 9000000 INFO @ Tue, 16 Jun 2020 08:29:26: 4000000 INFO @ Tue, 16 Jun 2020 08:29:29: 10000000 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 08:29:32: 5000000 INFO @ Tue, 16 Jun 2020 08:29:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.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 08:29:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:35: 11000000 INFO @ Tue, 16 Jun 2020 08:29:38: 6000000 INFO @ Tue, 16 Jun 2020 08:29:39: 1000000 INFO @ Tue, 16 Jun 2020 08:29:41: 12000000 INFO @ Tue, 16 Jun 2020 08:29:44: 7000000 INFO @ Tue, 16 Jun 2020 08:29:45: 2000000 INFO @ Tue, 16 Jun 2020 08:29:47: 13000000 INFO @ Tue, 16 Jun 2020 08:29:50: 8000000 INFO @ Tue, 16 Jun 2020 08:29:51: 3000000 INFO @ Tue, 16 Jun 2020 08:29:53: 14000000 INFO @ Tue, 16 Jun 2020 08:29:56: 9000000 INFO @ Tue, 16 Jun 2020 08:29:58: 4000000 INFO @ Tue, 16 Jun 2020 08:29:59: 15000000 INFO @ Tue, 16 Jun 2020 08:30:03: 10000000 INFO @ Tue, 16 Jun 2020 08:30:04: 5000000 INFO @ Tue, 16 Jun 2020 08:30:05: 16000000 INFO @ Tue, 16 Jun 2020 08:30:09: 11000000 INFO @ Tue, 16 Jun 2020 08:30:09: 6000000 INFO @ Tue, 16 Jun 2020 08:30:11: 17000000 INFO @ Tue, 16 Jun 2020 08:30:15: 12000000 INFO @ Tue, 16 Jun 2020 08:30:15: 7000000 INFO @ Tue, 16 Jun 2020 08:30:17: 18000000 INFO @ Tue, 16 Jun 2020 08:30:21: 13000000 INFO @ Tue, 16 Jun 2020 08:30:22: 8000000 INFO @ Tue, 16 Jun 2020 08:30:23: 19000000 INFO @ Tue, 16 Jun 2020 08:30:26: 14000000 INFO @ Tue, 16 Jun 2020 08:30:28: 9000000 INFO @ Tue, 16 Jun 2020 08:30:29: 20000000 INFO @ Tue, 16 Jun 2020 08:30:33: 15000000 INFO @ Tue, 16 Jun 2020 08:30:34: 10000000 INFO @ Tue, 16 Jun 2020 08:30:35: 21000000 INFO @ Tue, 16 Jun 2020 08:30:38: 16000000 INFO @ Tue, 16 Jun 2020 08:30:40: 11000000 INFO @ Tue, 16 Jun 2020 08:30:41: 22000000 INFO @ Tue, 16 Jun 2020 08:30:45: 17000000 INFO @ Tue, 16 Jun 2020 08:30:46: 12000000 INFO @ Tue, 16 Jun 2020 08:30:47: 23000000 INFO @ Tue, 16 Jun 2020 08:30:50: 18000000 INFO @ Tue, 16 Jun 2020 08:30:51: 13000000 INFO @ Tue, 16 Jun 2020 08:30:53: 24000000 INFO @ Tue, 16 Jun 2020 08:30:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:30:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:30:54: #1 total tags in treatment: 24111614 INFO @ Tue, 16 Jun 2020 08:30:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:54: #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 08:30:55: #1 tags after filtering in treatment: 24111614 INFO @ Tue, 16 Jun 2020 08:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:56: #2 number of paired peaks: 157 WARNING @ Tue, 16 Jun 2020 08:30:56: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:56: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:30:56: #2 alternative fragment length(s) may be 1,45,513 bps INFO @ Tue, 16 Jun 2020 08:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.05_model.r WARNING @ Tue, 16 Jun 2020 08:30:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:56: #2 You may need to consider one of the other alternative d(s): 1,45,513 WARNING @ Tue, 16 Jun 2020 08:30:56: #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 08:30:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:57: 19000000 INFO @ Tue, 16 Jun 2020 08:30:57: 14000000 INFO @ Tue, 16 Jun 2020 08:31:03: 20000000 INFO @ Tue, 16 Jun 2020 08:31:03: 15000000 INFO @ Tue, 16 Jun 2020 08:31:09: 21000000 INFO @ Tue, 16 Jun 2020 08:31:09: 16000000 INFO @ Tue, 16 Jun 2020 08:31:14: 22000000 INFO @ Tue, 16 Jun 2020 08:31:15: 17000000 INFO @ Tue, 16 Jun 2020 08:31:20: 23000000 INFO @ Tue, 16 Jun 2020 08:31:21: 18000000 INFO @ Tue, 16 Jun 2020 08:31:26: 24000000 INFO @ Tue, 16 Jun 2020 08:31:27: 19000000 INFO @ Tue, 16 Jun 2020 08:31:27: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:31:27: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:31:27: #1 total tags in treatment: 24111614 INFO @ Tue, 16 Jun 2020 08:31:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:27: #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 08:31:28: #1 tags after filtering in treatment: 24111614 INFO @ Tue, 16 Jun 2020 08:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:29: #2 number of paired peaks: 157 WARNING @ Tue, 16 Jun 2020 08:31:29: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:29: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:31:29: #2 alternative fragment length(s) may be 1,45,513 bps INFO @ Tue, 16 Jun 2020 08:31:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.10_model.r WARNING @ Tue, 16 Jun 2020 08:31:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:29: #2 You may need to consider one of the other alternative d(s): 1,45,513 WARNING @ Tue, 16 Jun 2020 08:31:29: #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 08:31:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:33: 20000000 INFO @ Tue, 16 Jun 2020 08:31:39: 21000000 INFO @ Tue, 16 Jun 2020 08:31:45: 22000000 INFO @ Tue, 16 Jun 2020 08:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:50: Done! INFO @ Tue, 16 Jun 2020 08:31:50: 23000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:56: 24000000 INFO @ Tue, 16 Jun 2020 08:31:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:31:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:31:57: #1 total tags in treatment: 24111614 INFO @ Tue, 16 Jun 2020 08:31:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:57: #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 08:31:57: #1 tags after filtering in treatment: 24111614 INFO @ Tue, 16 Jun 2020 08:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:58: #2 number of paired peaks: 157 WARNING @ Tue, 16 Jun 2020 08:31:58: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:59: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:31:59: #2 alternative fragment length(s) may be 1,45,513 bps INFO @ Tue, 16 Jun 2020 08:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.20_model.r WARNING @ Tue, 16 Jun 2020 08:31:59: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:59: #2 You may need to consider one of the other alternative d(s): 1,45,513 WARNING @ Tue, 16 Jun 2020 08:31:59: #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 08:31:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.10_summits.bed INFO @ Tue, 16 Jun 2020 08:32:21: Done! pass1 - making usageList (0 chroms): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257708/SRX257708.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:50: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling