Job ID = 12265612 SRX = SRX3029129 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:01:06 65633087 reads; of these: 65633087 (100.00%) were paired; of these: 35979126 (54.82%) aligned concordantly 0 times 24095397 (36.71%) aligned concordantly exactly 1 time 5558564 (8.47%) aligned concordantly >1 times ---- 35979126 pairs aligned concordantly 0 times; of these: 5317327 (14.78%) aligned discordantly 1 time ---- 30661799 pairs aligned 0 times concordantly or discordantly; of these: 61323598 mates make up the pairs; of these: 58352310 (95.15%) aligned 0 times 1167237 (1.90%) aligned exactly 1 time 1804051 (2.94%) aligned >1 times 55.55% overall alignment rate Time searching: 01:01:07 Overall time: 01:01:07 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 32 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] 17389526 / 34546971 = 0.5034 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 09:18:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.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 09:18:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:18:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:18:58: 1000000 INFO @ Sat, 03 Apr 2021 09:19:05: 2000000 INFO @ Sat, 03 Apr 2021 09:19:12: 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 09:19:19: 4000000 INFO @ Sat, 03 Apr 2021 09:19:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.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 09:19:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:19:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:19:27: 5000000 INFO @ Sat, 03 Apr 2021 09:19:31: 1000000 INFO @ Sat, 03 Apr 2021 09:19:35: 6000000 INFO @ Sat, 03 Apr 2021 09:19:40: 2000000 INFO @ Sat, 03 Apr 2021 09:19:42: 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 09:19:50: 8000000 INFO @ Sat, 03 Apr 2021 09:19:50: 3000000 INFO @ Sat, 03 Apr 2021 09:19:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.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 09:19:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:19:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:19:58: 9000000 INFO @ Sat, 03 Apr 2021 09:20:00: 4000000 INFO @ Sat, 03 Apr 2021 09:20:00: 1000000 INFO @ Sat, 03 Apr 2021 09:20:05: 10000000 INFO @ Sat, 03 Apr 2021 09:20:08: 2000000 INFO @ Sat, 03 Apr 2021 09:20:09: 5000000 INFO @ Sat, 03 Apr 2021 09:20:13: 11000000 INFO @ Sat, 03 Apr 2021 09:20:17: 3000000 INFO @ Sat, 03 Apr 2021 09:20:19: 6000000 INFO @ Sat, 03 Apr 2021 09:20:20: 12000000 INFO @ Sat, 03 Apr 2021 09:20:24: 4000000 INFO @ Sat, 03 Apr 2021 09:20:27: 13000000 INFO @ Sat, 03 Apr 2021 09:20:27: 7000000 INFO @ Sat, 03 Apr 2021 09:20:32: 5000000 INFO @ Sat, 03 Apr 2021 09:20:34: 14000000 INFO @ Sat, 03 Apr 2021 09:20:36: 8000000 INFO @ Sat, 03 Apr 2021 09:20:39: 6000000 INFO @ Sat, 03 Apr 2021 09:20:42: 15000000 INFO @ Sat, 03 Apr 2021 09:20:45: 9000000 INFO @ Sat, 03 Apr 2021 09:20:47: 7000000 INFO @ Sat, 03 Apr 2021 09:20:50: 16000000 INFO @ Sat, 03 Apr 2021 09:20:54: 10000000 INFO @ Sat, 03 Apr 2021 09:20:55: 8000000 INFO @ Sat, 03 Apr 2021 09:20:58: 17000000 INFO @ Sat, 03 Apr 2021 09:21:03: 9000000 INFO @ Sat, 03 Apr 2021 09:21:04: 11000000 INFO @ Sat, 03 Apr 2021 09:21:07: 18000000 INFO @ Sat, 03 Apr 2021 09:21:11: 10000000 INFO @ Sat, 03 Apr 2021 09:21:13: 12000000 INFO @ Sat, 03 Apr 2021 09:21:15: 19000000 INFO @ Sat, 03 Apr 2021 09:21:19: 11000000 INFO @ Sat, 03 Apr 2021 09:21:22: 13000000 INFO @ Sat, 03 Apr 2021 09:21:24: 20000000 INFO @ Sat, 03 Apr 2021 09:21:27: 12000000 INFO @ Sat, 03 Apr 2021 09:21:32: 14000000 INFO @ Sat, 03 Apr 2021 09:21:33: 21000000 INFO @ Sat, 03 Apr 2021 09:21:35: 13000000 INFO @ Sat, 03 Apr 2021 09:21:41: 15000000 INFO @ Sat, 03 Apr 2021 09:21:41: 22000000 INFO @ Sat, 03 Apr 2021 09:21:43: 14000000 INFO @ Sat, 03 Apr 2021 09:21:50: 23000000 INFO @ Sat, 03 Apr 2021 09:21:50: 16000000 INFO @ Sat, 03 Apr 2021 09:21:51: 15000000 INFO @ Sat, 03 Apr 2021 09:21:58: 24000000 INFO @ Sat, 03 Apr 2021 09:22:00: 17000000 INFO @ Sat, 03 Apr 2021 09:22:00: 16000000 INFO @ Sat, 03 Apr 2021 09:22:07: 25000000 INFO @ Sat, 03 Apr 2021 09:22:09: 17000000 INFO @ Sat, 03 Apr 2021 09:22:10: 18000000 INFO @ Sat, 03 Apr 2021 09:22:17: 26000000 INFO @ Sat, 03 Apr 2021 09:22:17: 18000000 INFO @ Sat, 03 Apr 2021 09:22:20: 19000000 INFO @ Sat, 03 Apr 2021 09:22:26: 27000000 INFO @ Sat, 03 Apr 2021 09:22:26: 19000000 INFO @ Sat, 03 Apr 2021 09:22:30: 20000000 INFO @ Sat, 03 Apr 2021 09:22:34: 28000000 INFO @ Sat, 03 Apr 2021 09:22:35: 20000000 INFO @ Sat, 03 Apr 2021 09:22:39: 21000000 INFO @ Sat, 03 Apr 2021 09:22:43: 29000000 INFO @ Sat, 03 Apr 2021 09:22:43: 21000000 INFO @ Sat, 03 Apr 2021 09:22:49: 22000000 INFO @ Sat, 03 Apr 2021 09:22:53: 30000000 INFO @ Sat, 03 Apr 2021 09:22:54: 22000000 INFO @ Sat, 03 Apr 2021 09:22:59: 23000000 INFO @ Sat, 03 Apr 2021 09:23:00: 31000000 INFO @ Sat, 03 Apr 2021 09:23:04: 23000000 INFO @ Sat, 03 Apr 2021 09:23:08: 32000000 INFO @ Sat, 03 Apr 2021 09:23:08: 24000000 INFO @ Sat, 03 Apr 2021 09:23:14: 24000000 INFO @ Sat, 03 Apr 2021 09:23:15: 33000000 INFO @ Sat, 03 Apr 2021 09:23:18: 25000000 INFO @ Sat, 03 Apr 2021 09:23:22: 34000000 INFO @ Sat, 03 Apr 2021 09:23:25: 25000000 INFO @ Sat, 03 Apr 2021 09:23:28: 26000000 INFO @ Sat, 03 Apr 2021 09:23:30: 35000000 INFO @ Sat, 03 Apr 2021 09:23:36: 26000000 INFO @ Sat, 03 Apr 2021 09:23:37: 36000000 INFO @ Sat, 03 Apr 2021 09:23:37: 27000000 INFO @ Sat, 03 Apr 2021 09:23:45: 37000000 INFO @ Sat, 03 Apr 2021 09:23:46: 27000000 INFO @ Sat, 03 Apr 2021 09:23:46: 28000000 INFO @ Sat, 03 Apr 2021 09:23:54: 38000000 INFO @ Sat, 03 Apr 2021 09:23:54: 28000000 INFO @ Sat, 03 Apr 2021 09:23:55: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:23:55: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:23:55: #1 total tags in treatment: 14908454 INFO @ Sat, 03 Apr 2021 09:23:55: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:23:55: #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 09:23:56: #1 tags after filtering in treatment: 9923397 INFO @ Sat, 03 Apr 2021 09:23:56: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 09:23:56: #1 finished! INFO @ Sat, 03 Apr 2021 09:23:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:23:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:23:56: 29000000 INFO @ Sat, 03 Apr 2021 09:23:56: #2 number of paired peaks: 754 WARNING @ Sat, 03 Apr 2021 09:23:56: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Sat, 03 Apr 2021 09:23:56: start model_add_line... INFO @ Sat, 03 Apr 2021 09:23:57: start X-correlation... INFO @ Sat, 03 Apr 2021 09:23:57: end of X-cor INFO @ Sat, 03 Apr 2021 09:23:57: #2 finished! INFO @ Sat, 03 Apr 2021 09:23:57: #2 predicted fragment length is 124 bps INFO @ Sat, 03 Apr 2021 09:23:57: #2 alternative fragment length(s) may be 124 bps INFO @ Sat, 03 Apr 2021 09:23:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.05_model.r WARNING @ Sat, 03 Apr 2021 09:23:57: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:23:57: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sat, 03 Apr 2021 09:23:57: #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 09:23:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:23:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:24:02: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:24:05: 30000000 INFO @ Sat, 03 Apr 2021 09:24:09: 30000000 INFO @ Sat, 03 Apr 2021 09:24:14: 31000000 INFO @ Sat, 03 Apr 2021 09:24:16: 31000000 INFO @ Sat, 03 Apr 2021 09:24:23: 32000000 INFO @ Sat, 03 Apr 2021 09:24:24: 32000000 INFO @ Sat, 03 Apr 2021 09:24:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:24:31: 33000000 INFO @ Sat, 03 Apr 2021 09:24:32: 33000000 INFO @ Sat, 03 Apr 2021 09:24:39: 34000000 INFO @ Sat, 03 Apr 2021 09:24:41: 34000000 INFO @ Sat, 03 Apr 2021 09:24:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:24:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:24:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.05_summits.bed INFO @ Sat, 03 Apr 2021 09:24:42: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (9353 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:24:46: 35000000 INFO @ Sat, 03 Apr 2021 09:24:51: 35000000 INFO @ Sat, 03 Apr 2021 09:24:53: 36000000 INFO @ Sat, 03 Apr 2021 09:25:00: 36000000 INFO @ Sat, 03 Apr 2021 09:25:01: 37000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:25:08: 38000000 INFO @ Sat, 03 Apr 2021 09:25:09: 37000000 INFO @ Sat, 03 Apr 2021 09:25:09: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:25:09: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:25:09: #1 total tags in treatment: 14908454 INFO @ Sat, 03 Apr 2021 09:25:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:25:09: #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 09:25:10: #1 tags after filtering in treatment: 9923397 INFO @ Sat, 03 Apr 2021 09:25:10: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 09:25:10: #1 finished! INFO @ Sat, 03 Apr 2021 09:25:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:25:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:25:10: #2 number of paired peaks: 754 WARNING @ Sat, 03 Apr 2021 09:25:10: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Sat, 03 Apr 2021 09:25:10: start model_add_line... INFO @ Sat, 03 Apr 2021 09:25:11: start X-correlation... INFO @ Sat, 03 Apr 2021 09:25:11: end of X-cor INFO @ Sat, 03 Apr 2021 09:25:11: #2 finished! INFO @ Sat, 03 Apr 2021 09:25:11: #2 predicted fragment length is 124 bps INFO @ Sat, 03 Apr 2021 09:25:11: #2 alternative fragment length(s) may be 124 bps INFO @ Sat, 03 Apr 2021 09:25:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.20_model.r WARNING @ Sat, 03 Apr 2021 09:25:11: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:25:11: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sat, 03 Apr 2021 09:25:11: #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 09:25:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:25:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:25:19: 38000000 INFO @ Sat, 03 Apr 2021 09:25:20: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:25:20: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:25:20: #1 total tags in treatment: 14908454 INFO @ Sat, 03 Apr 2021 09:25:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:25:20: #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 09:25:21: #1 tags after filtering in treatment: 9923397 INFO @ Sat, 03 Apr 2021 09:25:21: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 09:25:21: #1 finished! INFO @ Sat, 03 Apr 2021 09:25:21: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:25:22: #2 number of paired peaks: 754 WARNING @ Sat, 03 Apr 2021 09:25:22: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Sat, 03 Apr 2021 09:25:22: start model_add_line... INFO @ Sat, 03 Apr 2021 09:25:22: start X-correlation... INFO @ Sat, 03 Apr 2021 09:25:22: end of X-cor INFO @ Sat, 03 Apr 2021 09:25:22: #2 finished! INFO @ Sat, 03 Apr 2021 09:25:22: #2 predicted fragment length is 124 bps INFO @ Sat, 03 Apr 2021 09:25:22: #2 alternative fragment length(s) may be 124 bps INFO @ Sat, 03 Apr 2021 09:25:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.10_model.r WARNING @ Sat, 03 Apr 2021 09:25:22: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:25:22: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sat, 03 Apr 2021 09:25:22: #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 09:25:22: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:25:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:25:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:25:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:25:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:25:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.20_summits.bed INFO @ Sat, 03 Apr 2021 09:25:54: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2416 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:26:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:26:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:26:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029129/SRX3029129.10_summits.bed INFO @ Sat, 03 Apr 2021 09:26:05: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4997 records, 4 fields): 12 millis CompletedMACS2peakCalling