Job ID = 12265454 SRX = SRX2332995 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: 00:43:24 26099622 reads; of these: 26099622 (100.00%) were paired; of these: 12933341 (49.55%) aligned concordantly 0 times 10604489 (40.63%) aligned concordantly exactly 1 time 2561792 (9.82%) aligned concordantly >1 times ---- 12933341 pairs aligned concordantly 0 times; of these: 4514181 (34.90%) aligned discordantly 1 time ---- 8419160 pairs aligned 0 times concordantly or discordantly; of these: 16838320 mates make up the pairs; of these: 14574247 (86.55%) aligned 0 times 834740 (4.96%) aligned exactly 1 time 1429333 (8.49%) aligned >1 times 72.08% overall alignment rate Time searching: 00:43:24 Overall time: 00:43:24 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] 3373213 / 17587675 = 0.1918 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 08:08:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.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 08:08:48: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:08:48: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:08:54: 1000000 INFO @ Sat, 03 Apr 2021 08:09:01: 2000000 INFO @ Sat, 03 Apr 2021 08:09:07: 3000000 INFO @ Sat, 03 Apr 2021 08:09:13: 4000000 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 08:09:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.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 08:09:18: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:09:18: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:09:19: 5000000 INFO @ Sat, 03 Apr 2021 08:09:26: 1000000 INFO @ Sat, 03 Apr 2021 08:09:26: 6000000 INFO @ Sat, 03 Apr 2021 08:09:33: 2000000 INFO @ Sat, 03 Apr 2021 08:09:33: 7000000 INFO @ Sat, 03 Apr 2021 08:09:40: 3000000 INFO @ Sat, 03 Apr 2021 08:09:40: 8000000 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 08:09:47: 9000000 INFO @ Sat, 03 Apr 2021 08:09:47: 4000000 INFO @ Sat, 03 Apr 2021 08:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.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 08:09:48: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:09:48: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:09:54: 10000000 INFO @ Sat, 03 Apr 2021 08:09:55: 5000000 INFO @ Sat, 03 Apr 2021 08:09:56: 1000000 INFO @ Sat, 03 Apr 2021 08:10:02: 11000000 INFO @ Sat, 03 Apr 2021 08:10:02: 6000000 INFO @ Sat, 03 Apr 2021 08:10:04: 2000000 INFO @ Sat, 03 Apr 2021 08:10:10: 12000000 INFO @ Sat, 03 Apr 2021 08:10:10: 7000000 INFO @ Sat, 03 Apr 2021 08:10:12: 3000000 INFO @ Sat, 03 Apr 2021 08:10:18: 8000000 INFO @ Sat, 03 Apr 2021 08:10:18: 13000000 INFO @ Sat, 03 Apr 2021 08:10:20: 4000000 INFO @ Sat, 03 Apr 2021 08:10:25: 9000000 INFO @ Sat, 03 Apr 2021 08:10:26: 14000000 INFO @ Sat, 03 Apr 2021 08:10:27: 5000000 INFO @ Sat, 03 Apr 2021 08:10:33: 10000000 INFO @ Sat, 03 Apr 2021 08:10:34: 15000000 INFO @ Sat, 03 Apr 2021 08:10:35: 6000000 INFO @ Sat, 03 Apr 2021 08:10:41: 11000000 INFO @ Sat, 03 Apr 2021 08:10:41: 16000000 INFO @ Sat, 03 Apr 2021 08:10:43: 7000000 INFO @ Sat, 03 Apr 2021 08:10:49: 17000000 INFO @ Sat, 03 Apr 2021 08:10:49: 12000000 INFO @ Sat, 03 Apr 2021 08:10:51: 8000000 INFO @ Sat, 03 Apr 2021 08:10:57: 18000000 INFO @ Sat, 03 Apr 2021 08:10:57: 13000000 INFO @ Sat, 03 Apr 2021 08:10:59: 9000000 INFO @ Sat, 03 Apr 2021 08:11:05: 19000000 INFO @ Sat, 03 Apr 2021 08:11:05: 14000000 INFO @ Sat, 03 Apr 2021 08:11:07: 10000000 INFO @ Sat, 03 Apr 2021 08:11:13: 20000000 INFO @ Sat, 03 Apr 2021 08:11:13: 15000000 INFO @ Sat, 03 Apr 2021 08:11:15: 11000000 INFO @ Sat, 03 Apr 2021 08:11:20: 21000000 INFO @ Sat, 03 Apr 2021 08:11:21: 16000000 INFO @ Sat, 03 Apr 2021 08:11:23: 12000000 INFO @ Sat, 03 Apr 2021 08:11:28: 22000000 INFO @ Sat, 03 Apr 2021 08:11:29: 17000000 INFO @ Sat, 03 Apr 2021 08:11:31: 13000000 INFO @ Sat, 03 Apr 2021 08:11:36: 23000000 INFO @ Sat, 03 Apr 2021 08:11:37: 18000000 INFO @ Sat, 03 Apr 2021 08:11:39: 14000000 INFO @ Sat, 03 Apr 2021 08:11:44: 24000000 INFO @ Sat, 03 Apr 2021 08:11:45: 19000000 INFO @ Sat, 03 Apr 2021 08:11:47: 15000000 INFO @ Sat, 03 Apr 2021 08:11:52: 25000000 INFO @ Sat, 03 Apr 2021 08:11:53: 20000000 INFO @ Sat, 03 Apr 2021 08:11:55: 16000000 INFO @ Sat, 03 Apr 2021 08:12:00: 26000000 INFO @ Sat, 03 Apr 2021 08:12:01: 21000000 INFO @ Sat, 03 Apr 2021 08:12:03: 17000000 INFO @ Sat, 03 Apr 2021 08:12:08: 27000000 INFO @ Sat, 03 Apr 2021 08:12:09: 22000000 INFO @ Sat, 03 Apr 2021 08:12:11: 18000000 INFO @ Sat, 03 Apr 2021 08:12:16: 28000000 INFO @ Sat, 03 Apr 2021 08:12:16: 23000000 INFO @ Sat, 03 Apr 2021 08:12:19: 19000000 INFO @ Sat, 03 Apr 2021 08:12:24: 29000000 INFO @ Sat, 03 Apr 2021 08:12:24: 24000000 INFO @ Sat, 03 Apr 2021 08:12:27: 20000000 INFO @ Sat, 03 Apr 2021 08:12:32: 30000000 INFO @ Sat, 03 Apr 2021 08:12:32: 25000000 INFO @ Sat, 03 Apr 2021 08:12:35: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:12:39: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:12:39: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:12:39: #1 total tags in treatment: 10303131 INFO @ Sat, 03 Apr 2021 08:12:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:12:39: #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 08:12:40: #1 tags after filtering in treatment: 7000384 INFO @ Sat, 03 Apr 2021 08:12:40: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 08:12:40: #1 finished! INFO @ Sat, 03 Apr 2021 08:12:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:12:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:12:40: #2 number of paired peaks: 297 WARNING @ Sat, 03 Apr 2021 08:12:40: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sat, 03 Apr 2021 08:12:40: start model_add_line... INFO @ Sat, 03 Apr 2021 08:12:40: start X-correlation... INFO @ Sat, 03 Apr 2021 08:12:40: end of X-cor INFO @ Sat, 03 Apr 2021 08:12:40: #2 finished! INFO @ Sat, 03 Apr 2021 08:12:40: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Apr 2021 08:12:40: #2 alternative fragment length(s) may be 4,149,154 bps INFO @ Sat, 03 Apr 2021 08:12:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.05_model.r WARNING @ Sat, 03 Apr 2021 08:12:40: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:12:40: #2 You may need to consider one of the other alternative d(s): 4,149,154 WARNING @ Sat, 03 Apr 2021 08:12:40: #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 08:12:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:12:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:12:41: 26000000 INFO @ Sat, 03 Apr 2021 08:12:42: 22000000 INFO @ Sat, 03 Apr 2021 08:12:48: 27000000 INFO @ Sat, 03 Apr 2021 08:12:50: 23000000 INFO @ Sat, 03 Apr 2021 08:12:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:12:55: 28000000 INFO @ Sat, 03 Apr 2021 08:12:57: 24000000 INFO @ Sat, 03 Apr 2021 08:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.05_summits.bed INFO @ Sat, 03 Apr 2021 08:13:02: Done! INFO @ Sat, 03 Apr 2021 08:13:03: 29000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1894 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:13:04: 25000000 INFO @ Sat, 03 Apr 2021 08:13:10: 30000000 INFO @ Sat, 03 Apr 2021 08:13:11: 26000000 INFO @ Sat, 03 Apr 2021 08:13:15: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:13:15: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:13:15: #1 total tags in treatment: 10303131 INFO @ Sat, 03 Apr 2021 08:13:15: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:13:15: #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 08:13:16: #1 tags after filtering in treatment: 7000384 INFO @ Sat, 03 Apr 2021 08:13:16: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 08:13:16: #1 finished! INFO @ Sat, 03 Apr 2021 08:13:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:13:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:13:16: #2 number of paired peaks: 297 WARNING @ Sat, 03 Apr 2021 08:13:16: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sat, 03 Apr 2021 08:13:16: start model_add_line... INFO @ Sat, 03 Apr 2021 08:13:16: start X-correlation... INFO @ Sat, 03 Apr 2021 08:13:16: end of X-cor INFO @ Sat, 03 Apr 2021 08:13:16: #2 finished! INFO @ Sat, 03 Apr 2021 08:13:16: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Apr 2021 08:13:16: #2 alternative fragment length(s) may be 4,149,154 bps INFO @ Sat, 03 Apr 2021 08:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.10_model.r WARNING @ Sat, 03 Apr 2021 08:13:16: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:13:16: #2 You may need to consider one of the other alternative d(s): 4,149,154 WARNING @ Sat, 03 Apr 2021 08:13:16: #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 08:13:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:13:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:13:17: 27000000 INFO @ Sat, 03 Apr 2021 08:13:23: 28000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:13:30: 29000000 INFO @ Sat, 03 Apr 2021 08:13:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:13:36: 30000000 INFO @ Sat, 03 Apr 2021 08:13:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:13:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:13:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.10_summits.bed INFO @ Sat, 03 Apr 2021 08:13:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (695 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:13:41: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:13:41: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:13:41: #1 total tags in treatment: 10303131 INFO @ Sat, 03 Apr 2021 08:13:41: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:13:41: #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 08:13:41: #1 tags after filtering in treatment: 7000384 INFO @ Sat, 03 Apr 2021 08:13:41: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 08:13:41: #1 finished! INFO @ Sat, 03 Apr 2021 08:13:41: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:13:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:13:42: #2 number of paired peaks: 297 WARNING @ Sat, 03 Apr 2021 08:13:42: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sat, 03 Apr 2021 08:13:42: start model_add_line... INFO @ Sat, 03 Apr 2021 08:13:42: start X-correlation... INFO @ Sat, 03 Apr 2021 08:13:42: end of X-cor INFO @ Sat, 03 Apr 2021 08:13:42: #2 finished! INFO @ Sat, 03 Apr 2021 08:13:42: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Apr 2021 08:13:42: #2 alternative fragment length(s) may be 4,149,154 bps INFO @ Sat, 03 Apr 2021 08:13:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.20_model.r WARNING @ Sat, 03 Apr 2021 08:13:42: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:13:42: #2 You may need to consider one of the other alternative d(s): 4,149,154 WARNING @ Sat, 03 Apr 2021 08:13:42: #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 08:13:42: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:13:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:13:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:14:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:14:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:14:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332995/SRX2332995.20_summits.bed INFO @ Sat, 03 Apr 2021 08:14:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 1 millis CompletedMACS2peakCalling