Job ID = 10165893 SRX = SRX7879259 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:06:34 30104381 reads; of these: 30104381 (100.00%) were unpaired; of these: 446035 (1.48%) aligned 0 times 24722504 (82.12%) aligned exactly 1 time 4935842 (16.40%) aligned >1 times 98.52% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 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 16 files... [bam_rmdupse_core] 4396419 / 29658346 = 0.1482 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 @ Thu, 08 Oct 2020 20:20:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.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 @ Thu, 08 Oct 2020 20:20:09: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:20:09: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:20:16: 1000000 INFO @ Thu, 08 Oct 2020 20:20:22: 2000000 INFO @ Thu, 08 Oct 2020 20:20:28: 3000000 INFO @ Thu, 08 Oct 2020 20:20:34: 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 @ Thu, 08 Oct 2020 20:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.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 @ Thu, 08 Oct 2020 20:20:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:20:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:20:41: 5000000 INFO @ Thu, 08 Oct 2020 20:20:46: 1000000 INFO @ Thu, 08 Oct 2020 20:20:48: 6000000 INFO @ Thu, 08 Oct 2020 20:20:52: 2000000 INFO @ Thu, 08 Oct 2020 20:20:54: 7000000 INFO @ Thu, 08 Oct 2020 20:20:59: 3000000 INFO @ Thu, 08 Oct 2020 20:21:01: 8000000 INFO @ Thu, 08 Oct 2020 20:21:05: 4000000 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 @ Thu, 08 Oct 2020 20:21:08: 9000000 INFO @ Thu, 08 Oct 2020 20:21:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.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 @ Thu, 08 Oct 2020 20:21:09: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:21:09: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:21:12: 5000000 INFO @ Thu, 08 Oct 2020 20:21:15: 10000000 INFO @ Thu, 08 Oct 2020 20:21:16: 1000000 INFO @ Thu, 08 Oct 2020 20:21:19: 6000000 INFO @ Thu, 08 Oct 2020 20:21:22: 11000000 INFO @ Thu, 08 Oct 2020 20:21:23: 2000000 INFO @ Thu, 08 Oct 2020 20:21:26: 7000000 INFO @ Thu, 08 Oct 2020 20:21:29: 12000000 INFO @ Thu, 08 Oct 2020 20:21:30: 3000000 INFO @ Thu, 08 Oct 2020 20:21:33: 8000000 INFO @ Thu, 08 Oct 2020 20:21:36: 13000000 INFO @ Thu, 08 Oct 2020 20:21:37: 4000000 INFO @ Thu, 08 Oct 2020 20:21:39: 9000000 INFO @ Thu, 08 Oct 2020 20:21:43: 14000000 INFO @ Thu, 08 Oct 2020 20:21:44: 5000000 INFO @ Thu, 08 Oct 2020 20:21:46: 10000000 INFO @ Thu, 08 Oct 2020 20:21:50: 15000000 INFO @ Thu, 08 Oct 2020 20:21:50: 6000000 INFO @ Thu, 08 Oct 2020 20:21:53: 11000000 INFO @ Thu, 08 Oct 2020 20:21:57: 7000000 INFO @ Thu, 08 Oct 2020 20:21:57: 16000000 INFO @ Thu, 08 Oct 2020 20:22:00: 12000000 INFO @ Thu, 08 Oct 2020 20:22:04: 8000000 INFO @ Thu, 08 Oct 2020 20:22:04: 17000000 INFO @ Thu, 08 Oct 2020 20:22:07: 13000000 INFO @ Thu, 08 Oct 2020 20:22:11: 9000000 INFO @ Thu, 08 Oct 2020 20:22:11: 18000000 INFO @ Thu, 08 Oct 2020 20:22:14: 14000000 INFO @ Thu, 08 Oct 2020 20:22:18: 10000000 INFO @ Thu, 08 Oct 2020 20:22:18: 19000000 INFO @ Thu, 08 Oct 2020 20:22:21: 15000000 INFO @ Thu, 08 Oct 2020 20:22:25: 11000000 INFO @ Thu, 08 Oct 2020 20:22:25: 20000000 INFO @ Thu, 08 Oct 2020 20:22:27: 16000000 INFO @ Thu, 08 Oct 2020 20:22:31: 12000000 INFO @ Thu, 08 Oct 2020 20:22:32: 21000000 INFO @ Thu, 08 Oct 2020 20:22:34: 17000000 INFO @ Thu, 08 Oct 2020 20:22:38: 13000000 INFO @ Thu, 08 Oct 2020 20:22:39: 22000000 INFO @ Thu, 08 Oct 2020 20:22:41: 18000000 INFO @ Thu, 08 Oct 2020 20:22:45: 14000000 INFO @ Thu, 08 Oct 2020 20:22:46: 23000000 INFO @ Thu, 08 Oct 2020 20:22:48: 19000000 INFO @ Thu, 08 Oct 2020 20:22:52: 15000000 INFO @ Thu, 08 Oct 2020 20:22:54: 24000000 INFO @ Thu, 08 Oct 2020 20:22:55: 20000000 INFO @ Thu, 08 Oct 2020 20:22:59: 16000000 INFO @ Thu, 08 Oct 2020 20:23:01: 25000000 INFO @ Thu, 08 Oct 2020 20:23:01: 21000000 INFO @ Thu, 08 Oct 2020 20:23:02: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:23:02: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:23:02: #1 total tags in treatment: 25261927 INFO @ Thu, 08 Oct 2020 20:23:02: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:23:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:23:03: #1 tags after filtering in treatment: 25261927 INFO @ Thu, 08 Oct 2020 20:23:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:23:03: #1 finished! INFO @ Thu, 08 Oct 2020 20:23:03: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:23:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:23:04: #2 number of paired peaks: 145 WARNING @ Thu, 08 Oct 2020 20:23:04: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Thu, 08 Oct 2020 20:23:04: start model_add_line... INFO @ Thu, 08 Oct 2020 20:23:05: start X-correlation... INFO @ Thu, 08 Oct 2020 20:23:05: end of X-cor INFO @ Thu, 08 Oct 2020 20:23:05: #2 finished! INFO @ Thu, 08 Oct 2020 20:23:05: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:23:05: #2 alternative fragment length(s) may be 1,14,33,191,478,535,574,589,596 bps INFO @ Thu, 08 Oct 2020 20:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.05_model.r WARNING @ Thu, 08 Oct 2020 20:23:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:23:05: #2 You may need to consider one of the other alternative d(s): 1,14,33,191,478,535,574,589,596 WARNING @ Thu, 08 Oct 2020 20:23:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:23:05: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:23:06: 17000000 INFO @ Thu, 08 Oct 2020 20:23:08: 22000000 INFO @ Thu, 08 Oct 2020 20:23:13: 18000000 INFO @ Thu, 08 Oct 2020 20:23:15: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:23:19: 19000000 INFO @ Thu, 08 Oct 2020 20:23:22: 24000000 INFO @ Thu, 08 Oct 2020 20:23:26: 20000000 INFO @ Thu, 08 Oct 2020 20:23:29: 25000000 INFO @ Thu, 08 Oct 2020 20:23:30: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:23:30: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:23:30: #1 total tags in treatment: 25261927 INFO @ Thu, 08 Oct 2020 20:23:30: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:23:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:23:31: #1 tags after filtering in treatment: 25261927 INFO @ Thu, 08 Oct 2020 20:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:23:31: #1 finished! INFO @ Thu, 08 Oct 2020 20:23:31: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:23:32: #2 number of paired peaks: 145 WARNING @ Thu, 08 Oct 2020 20:23:32: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Thu, 08 Oct 2020 20:23:32: start model_add_line... INFO @ Thu, 08 Oct 2020 20:23:33: start X-correlation... INFO @ Thu, 08 Oct 2020 20:23:33: end of X-cor INFO @ Thu, 08 Oct 2020 20:23:33: #2 finished! INFO @ Thu, 08 Oct 2020 20:23:33: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:23:33: #2 alternative fragment length(s) may be 1,14,33,191,478,535,574,589,596 bps INFO @ Thu, 08 Oct 2020 20:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.10_model.r WARNING @ Thu, 08 Oct 2020 20:23:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:23:33: #2 You may need to consider one of the other alternative d(s): 1,14,33,191,478,535,574,589,596 WARNING @ Thu, 08 Oct 2020 20:23:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:23:33: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:23:33: 21000000 INFO @ Thu, 08 Oct 2020 20:23:39: 22000000 INFO @ Thu, 08 Oct 2020 20:23:44: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:23:45: 23000000 INFO @ Thu, 08 Oct 2020 20:23:51: 24000000 INFO @ Thu, 08 Oct 2020 20:23:57: 25000000 INFO @ Thu, 08 Oct 2020 20:23:59: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:23:59: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:23:59: #1 total tags in treatment: 25261927 INFO @ Thu, 08 Oct 2020 20:23:59: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:23:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:23:59: #1 tags after filtering in treatment: 25261927 INFO @ Thu, 08 Oct 2020 20:23:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:23:59: #1 finished! INFO @ Thu, 08 Oct 2020 20:23:59: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:23:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:24:01: #2 number of paired peaks: 145 WARNING @ Thu, 08 Oct 2020 20:24:01: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Thu, 08 Oct 2020 20:24:01: start model_add_line... INFO @ Thu, 08 Oct 2020 20:24:01: start X-correlation... INFO @ Thu, 08 Oct 2020 20:24:01: end of X-cor INFO @ Thu, 08 Oct 2020 20:24:01: #2 finished! INFO @ Thu, 08 Oct 2020 20:24:01: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:24:01: #2 alternative fragment length(s) may be 1,14,33,191,478,535,574,589,596 bps INFO @ Thu, 08 Oct 2020 20:24:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.20_model.r WARNING @ Thu, 08 Oct 2020 20:24:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:24:01: #2 You may need to consider one of the other alternative d(s): 1,14,33,191,478,535,574,589,596 WARNING @ Thu, 08 Oct 2020 20:24:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:24:01: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:24:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:24:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:24:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:24:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.05_summits.bed INFO @ Thu, 08 Oct 2020 20:24:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:24:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:24:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:24:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:24:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.10_summits.bed INFO @ Thu, 08 Oct 2020 20:24:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:24:40: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:24:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:24:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:24:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7879259/SRX7879259.20_summits.bed INFO @ Thu, 08 Oct 2020 20:24:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling