Job ID = 12265500 SRX = SRX7246269 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: 00:00:00 Multiseed full-index search: 00:37:10 23264534 reads; of these: 23264534 (100.00%) were paired; of these: 11541701 (49.61%) aligned concordantly 0 times 9801430 (42.13%) aligned concordantly exactly 1 time 1921403 (8.26%) aligned concordantly >1 times ---- 11541701 pairs aligned concordantly 0 times; of these: 3172243 (27.49%) aligned discordantly 1 time ---- 8369458 pairs aligned 0 times concordantly or discordantly; of these: 16738916 mates make up the pairs; of these: 15114775 (90.30%) aligned 0 times 551580 (3.30%) aligned exactly 1 time 1072561 (6.41%) aligned >1 times 67.52% overall alignment rate Time searching: 00:37:10 Overall time: 00:37:10 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 24 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] 3978130 / 14795380 = 0.2689 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 08:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.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 08:10:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:10:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:11:01: 1000000 INFO @ Sat, 03 Apr 2021 08:11:08: 2000000 INFO @ Sat, 03 Apr 2021 08:11:16: 3000000 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 08:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.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 08:11:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:11:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:11:23: 4000000 INFO @ Sat, 03 Apr 2021 08:11:31: 1000000 INFO @ Sat, 03 Apr 2021 08:11:32: 5000000 INFO @ Sat, 03 Apr 2021 08:11:40: 2000000 INFO @ Sat, 03 Apr 2021 08:11:40: 6000000 INFO @ Sat, 03 Apr 2021 08:11:48: 3000000 INFO @ Sat, 03 Apr 2021 08:11:48: 7000000 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 08:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.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 08:11:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:11:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:11:57: 4000000 INFO @ Sat, 03 Apr 2021 08:11:57: 8000000 INFO @ Sat, 03 Apr 2021 08:12:04: 1000000 INFO @ Sat, 03 Apr 2021 08:12:05: 5000000 INFO @ Sat, 03 Apr 2021 08:12:06: 9000000 INFO @ Sat, 03 Apr 2021 08:12:14: 6000000 INFO @ Sat, 03 Apr 2021 08:12:14: 2000000 INFO @ Sat, 03 Apr 2021 08:12:15: 10000000 INFO @ Sat, 03 Apr 2021 08:12:23: 7000000 INFO @ Sat, 03 Apr 2021 08:12:24: 11000000 INFO @ Sat, 03 Apr 2021 08:12:25: 3000000 INFO @ Sat, 03 Apr 2021 08:12:32: 8000000 INFO @ Sat, 03 Apr 2021 08:12:33: 12000000 INFO @ Sat, 03 Apr 2021 08:12:36: 4000000 INFO @ Sat, 03 Apr 2021 08:12:41: 9000000 INFO @ Sat, 03 Apr 2021 08:12:41: 13000000 INFO @ Sat, 03 Apr 2021 08:12:46: 5000000 INFO @ Sat, 03 Apr 2021 08:12:50: 14000000 INFO @ Sat, 03 Apr 2021 08:12:50: 10000000 INFO @ Sat, 03 Apr 2021 08:12:57: 6000000 INFO @ Sat, 03 Apr 2021 08:12:59: 15000000 INFO @ Sat, 03 Apr 2021 08:12:59: 11000000 INFO @ Sat, 03 Apr 2021 08:13:07: 7000000 INFO @ Sat, 03 Apr 2021 08:13:07: 16000000 INFO @ Sat, 03 Apr 2021 08:13:07: 12000000 INFO @ Sat, 03 Apr 2021 08:13:16: 17000000 INFO @ Sat, 03 Apr 2021 08:13:16: 13000000 INFO @ Sat, 03 Apr 2021 08:13:18: 8000000 INFO @ Sat, 03 Apr 2021 08:13:25: 18000000 INFO @ Sat, 03 Apr 2021 08:13:25: 14000000 INFO @ Sat, 03 Apr 2021 08:13:29: 9000000 INFO @ Sat, 03 Apr 2021 08:13:34: 19000000 INFO @ Sat, 03 Apr 2021 08:13:34: 15000000 INFO @ Sat, 03 Apr 2021 08:13:39: 10000000 INFO @ Sat, 03 Apr 2021 08:13:42: 20000000 INFO @ Sat, 03 Apr 2021 08:13:42: 16000000 INFO @ Sat, 03 Apr 2021 08:13:49: 11000000 INFO @ Sat, 03 Apr 2021 08:13:51: 17000000 INFO @ Sat, 03 Apr 2021 08:13:51: 21000000 INFO @ Sat, 03 Apr 2021 08:14:00: 12000000 INFO @ Sat, 03 Apr 2021 08:14:00: 18000000 INFO @ Sat, 03 Apr 2021 08:14:00: 22000000 INFO @ Sat, 03 Apr 2021 08:14:08: 19000000 INFO @ Sat, 03 Apr 2021 08:14:09: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:14:10: 13000000 INFO @ Sat, 03 Apr 2021 08:14:13: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:14:13: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:14:13: #1 total tags in treatment: 8465737 INFO @ Sat, 03 Apr 2021 08:14:13: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:14:13: #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 08:14:14: #1 tags after filtering in treatment: 6331829 INFO @ Sat, 03 Apr 2021 08:14:14: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 08:14:14: #1 finished! INFO @ Sat, 03 Apr 2021 08:14:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:14:14: #2 number of paired peaks: 958 WARNING @ Sat, 03 Apr 2021 08:14:14: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sat, 03 Apr 2021 08:14:14: start model_add_line... INFO @ Sat, 03 Apr 2021 08:14:14: start X-correlation... INFO @ Sat, 03 Apr 2021 08:14:14: end of X-cor INFO @ Sat, 03 Apr 2021 08:14:14: #2 finished! INFO @ Sat, 03 Apr 2021 08:14:14: #2 predicted fragment length is 190 bps INFO @ Sat, 03 Apr 2021 08:14:14: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 03 Apr 2021 08:14:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.05_model.r WARNING @ Sat, 03 Apr 2021 08:14:14: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:14:14: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Sat, 03 Apr 2021 08:14:14: #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 08:14:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:14:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:14:17: 20000000 INFO @ Sat, 03 Apr 2021 08:14:20: 14000000 INFO @ Sat, 03 Apr 2021 08:14:26: 21000000 INFO @ Sat, 03 Apr 2021 08:14:30: 15000000 INFO @ Sat, 03 Apr 2021 08:14:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:14:35: 22000000 INFO @ Sat, 03 Apr 2021 08:14:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:14:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:14:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.05_summits.bed INFO @ Sat, 03 Apr 2021 08:14:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4014 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:14:41: 16000000 INFO @ Sat, 03 Apr 2021 08:14:44: 23000000 INFO @ Sat, 03 Apr 2021 08:14:48: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:14:48: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:14:48: #1 total tags in treatment: 8465737 INFO @ Sat, 03 Apr 2021 08:14:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:14:48: #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 08:14:48: #1 tags after filtering in treatment: 6331829 INFO @ Sat, 03 Apr 2021 08:14:48: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 08:14:48: #1 finished! INFO @ Sat, 03 Apr 2021 08:14:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:14:48: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:14:48: #2 number of paired peaks: 958 WARNING @ Sat, 03 Apr 2021 08:14:48: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sat, 03 Apr 2021 08:14:48: start model_add_line... INFO @ Sat, 03 Apr 2021 08:14:48: start X-correlation... INFO @ Sat, 03 Apr 2021 08:14:48: end of X-cor INFO @ Sat, 03 Apr 2021 08:14:48: #2 finished! INFO @ Sat, 03 Apr 2021 08:14:48: #2 predicted fragment length is 190 bps INFO @ Sat, 03 Apr 2021 08:14:48: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 03 Apr 2021 08:14:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.10_model.r WARNING @ Sat, 03 Apr 2021 08:14:48: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:14:48: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Sat, 03 Apr 2021 08:14:48: #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 08:14:48: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:14:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:14:51: 17000000 INFO @ Sat, 03 Apr 2021 08:15:00: 18000000 INFO @ Sat, 03 Apr 2021 08:15:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:15:10: 19000000 INFO @ Sat, 03 Apr 2021 08:15:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:15:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:15:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.10_summits.bed INFO @ Sat, 03 Apr 2021 08:15:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2294 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:15:19: 20000000 INFO @ Sat, 03 Apr 2021 08:15:29: 21000000 INFO @ Sat, 03 Apr 2021 08:15:39: 22000000 INFO @ Sat, 03 Apr 2021 08:15:49: 23000000 INFO @ Sat, 03 Apr 2021 08:15:54: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:15:54: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:15:54: #1 total tags in treatment: 8465737 INFO @ Sat, 03 Apr 2021 08:15:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:15:54: #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 08:15:54: #1 tags after filtering in treatment: 6331829 INFO @ Sat, 03 Apr 2021 08:15:54: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 08:15:54: #1 finished! INFO @ Sat, 03 Apr 2021 08:15:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:15:55: #2 number of paired peaks: 958 WARNING @ Sat, 03 Apr 2021 08:15:55: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sat, 03 Apr 2021 08:15:55: start model_add_line... INFO @ Sat, 03 Apr 2021 08:15:55: start X-correlation... INFO @ Sat, 03 Apr 2021 08:15:55: end of X-cor INFO @ Sat, 03 Apr 2021 08:15:55: #2 finished! INFO @ Sat, 03 Apr 2021 08:15:55: #2 predicted fragment length is 190 bps INFO @ Sat, 03 Apr 2021 08:15:55: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 03 Apr 2021 08:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.20_model.r WARNING @ Sat, 03 Apr 2021 08:15:55: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:15:55: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Sat, 03 Apr 2021 08:15:55: #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 08:15:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:16:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:16:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:16:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:16:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246269/SRX7246269.20_summits.bed INFO @ Sat, 03 Apr 2021 08:16:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1021 records, 4 fields): 3 millis CompletedMACS2peakCalling