Job ID = 12265377 SRX = SRX7687154 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED 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: 00:00:01 Multiseed full-index search: 00:20:01 22511278 reads; of these: 22511278 (100.00%) were paired; of these: 5883279 (26.13%) aligned concordantly 0 times 14692384 (65.27%) aligned concordantly exactly 1 time 1935615 (8.60%) aligned concordantly >1 times ---- 5883279 pairs aligned concordantly 0 times; of these: 1562388 (26.56%) aligned discordantly 1 time ---- 4320891 pairs aligned 0 times concordantly or discordantly; of these: 8641782 mates make up the pairs; of these: 8083637 (93.54%) aligned 0 times 262005 (3.03%) aligned exactly 1 time 296140 (3.43%) aligned >1 times 82.05% overall alignment rate Time searching: 00:20:02 Overall time: 00:20:02 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 12604829 / 18149187 = 0.6945 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.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 @ Sat, 03 Apr 2021 07:11:10: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:11:10: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:11:16: 1000000 INFO @ Sat, 03 Apr 2021 07:11:21: 2000000 INFO @ Sat, 03 Apr 2021 07:11:26: 3000000 INFO @ Sat, 03 Apr 2021 07:11:32: 4000000 INFO @ Sat, 03 Apr 2021 07:11:37: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.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 @ Sat, 03 Apr 2021 07:11:40: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:11:40: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:11:43: 6000000 INFO @ Sat, 03 Apr 2021 07:11:47: 1000000 INFO @ Sat, 03 Apr 2021 07:11:49: 7000000 INFO @ Sat, 03 Apr 2021 07:11:54: 2000000 INFO @ Sat, 03 Apr 2021 07:11:55: 8000000 INFO @ Sat, 03 Apr 2021 07:12:02: 3000000 INFO @ Sat, 03 Apr 2021 07:12:02: 9000000 INFO @ Sat, 03 Apr 2021 07:12:08: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:12:09: 4000000 INFO @ Sat, 03 Apr 2021 07:12:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.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 @ Sat, 03 Apr 2021 07:12:10: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:12:10: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:12:14: 11000000 INFO @ Sat, 03 Apr 2021 07:12:16: 5000000 INFO @ Sat, 03 Apr 2021 07:12:18: 1000000 INFO @ Sat, 03 Apr 2021 07:12:19: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:12:19: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:12:19: #1 total tags in treatment: 4970856 INFO @ Sat, 03 Apr 2021 07:12:19: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:12:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:12:19: #1 tags after filtering in treatment: 3850755 INFO @ Sat, 03 Apr 2021 07:12:19: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 07:12:19: #1 finished! INFO @ Sat, 03 Apr 2021 07:12:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:12:19: #2 number of paired peaks: 563 WARNING @ Sat, 03 Apr 2021 07:12:19: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sat, 03 Apr 2021 07:12:19: start model_add_line... INFO @ Sat, 03 Apr 2021 07:12:19: start X-correlation... INFO @ Sat, 03 Apr 2021 07:12:19: end of X-cor INFO @ Sat, 03 Apr 2021 07:12:19: #2 finished! INFO @ Sat, 03 Apr 2021 07:12:19: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 07:12:19: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Apr 2021 07:12:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.05_model.r WARNING @ Sat, 03 Apr 2021 07:12:19: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:12:19: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 03 Apr 2021 07:12:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:12:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:12:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:12:23: 6000000 INFO @ Sat, 03 Apr 2021 07:12:25: 2000000 INFO @ Sat, 03 Apr 2021 07:12:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:12:30: 7000000 INFO @ Sat, 03 Apr 2021 07:12:32: 3000000 INFO @ Sat, 03 Apr 2021 07:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.05_summits.bed INFO @ Sat, 03 Apr 2021 07:12:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (732 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:12:37: 8000000 INFO @ Sat, 03 Apr 2021 07:12:39: 4000000 INFO @ Sat, 03 Apr 2021 07:12:44: 9000000 INFO @ Sat, 03 Apr 2021 07:12:46: 5000000 INFO @ Sat, 03 Apr 2021 07:12:52: 10000000 INFO @ Sat, 03 Apr 2021 07:12:53: 6000000 INFO @ Sat, 03 Apr 2021 07:12:58: 11000000 INFO @ Sat, 03 Apr 2021 07:13:00: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:13:03: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:13:03: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:13:03: #1 total tags in treatment: 4970856 INFO @ Sat, 03 Apr 2021 07:13:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:13:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:13:03: #1 tags after filtering in treatment: 3850755 INFO @ Sat, 03 Apr 2021 07:13:03: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 07:13:03: #1 finished! INFO @ Sat, 03 Apr 2021 07:13:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:13:03: #2 number of paired peaks: 563 WARNING @ Sat, 03 Apr 2021 07:13:03: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sat, 03 Apr 2021 07:13:03: start model_add_line... INFO @ Sat, 03 Apr 2021 07:13:04: start X-correlation... INFO @ Sat, 03 Apr 2021 07:13:04: end of X-cor INFO @ Sat, 03 Apr 2021 07:13:04: #2 finished! INFO @ Sat, 03 Apr 2021 07:13:04: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 07:13:04: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Apr 2021 07:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.10_model.r WARNING @ Sat, 03 Apr 2021 07:13:04: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:13:04: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 03 Apr 2021 07:13:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:13:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:13:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:13:07: 8000000 INFO @ Sat, 03 Apr 2021 07:13:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:13:14: 9000000 INFO @ Sat, 03 Apr 2021 07:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:13:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.10_summits.bed INFO @ Sat, 03 Apr 2021 07:13:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (370 records, 4 fields): 38 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:13:20: 10000000 INFO @ Sat, 03 Apr 2021 07:13:27: 11000000 INFO @ Sat, 03 Apr 2021 07:13:31: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:13:31: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:13:31: #1 total tags in treatment: 4970856 INFO @ Sat, 03 Apr 2021 07:13:31: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:13:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:13:31: #1 tags after filtering in treatment: 3850755 INFO @ Sat, 03 Apr 2021 07:13:31: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 07:13:31: #1 finished! INFO @ Sat, 03 Apr 2021 07:13:31: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:13:32: #2 number of paired peaks: 563 WARNING @ Sat, 03 Apr 2021 07:13:32: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sat, 03 Apr 2021 07:13:32: start model_add_line... INFO @ Sat, 03 Apr 2021 07:13:32: start X-correlation... INFO @ Sat, 03 Apr 2021 07:13:32: end of X-cor INFO @ Sat, 03 Apr 2021 07:13:32: #2 finished! INFO @ Sat, 03 Apr 2021 07:13:32: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 07:13:32: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Apr 2021 07:13:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.20_model.r WARNING @ Sat, 03 Apr 2021 07:13:32: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:13:32: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 03 Apr 2021 07:13:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:13:32: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:13:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:13:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:13:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:13:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:13:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687154/SRX7687154.20_summits.bed INFO @ Sat, 03 Apr 2021 07:13:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (148 records, 4 fields): 14 millis CompletedMACS2peakCalling