Job ID = 16434987 SRX = SRX13336913 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: 01:00:40 24637370 reads; of these: 24637370 (100.00%) were paired; of these: 10076380 (40.90%) aligned concordantly 0 times 12414399 (50.39%) aligned concordantly exactly 1 time 2146591 (8.71%) aligned concordantly >1 times ---- 10076380 pairs aligned concordantly 0 times; of these: 4648517 (46.13%) aligned discordantly 1 time ---- 5427863 pairs aligned 0 times concordantly or discordantly; of these: 10855726 mates make up the pairs; of these: 9194555 (84.70%) aligned 0 times 740535 (6.82%) aligned exactly 1 time 920636 (8.48%) aligned >1 times 81.34% overall alignment rate Time searching: 01:00:40 Overall time: 01:00:40 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] 2552987 / 19130897 = 0.1334 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:51:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.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 @ Tue, 02 Aug 2022 11:51:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:51:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:51:13: 1000000 INFO @ Tue, 02 Aug 2022 11:51:26: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.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 @ Tue, 02 Aug 2022 11:51:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:51:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:51:39: 3000000 INFO @ Tue, 02 Aug 2022 11:51:42: 1000000 INFO @ Tue, 02 Aug 2022 11:51:53: 4000000 INFO @ Tue, 02 Aug 2022 11:51:54: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:52:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.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 @ Tue, 02 Aug 2022 11:52:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:52:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:52:07: 3000000 INFO @ Tue, 02 Aug 2022 11:52:08: 5000000 INFO @ Tue, 02 Aug 2022 11:52:16: 1000000 INFO @ Tue, 02 Aug 2022 11:52:19: 4000000 INFO @ Tue, 02 Aug 2022 11:52:22: 6000000 INFO @ Tue, 02 Aug 2022 11:52:31: 5000000 INFO @ Tue, 02 Aug 2022 11:52:32: 2000000 INFO @ Tue, 02 Aug 2022 11:52:37: 7000000 INFO @ Tue, 02 Aug 2022 11:52:43: 6000000 INFO @ Tue, 02 Aug 2022 11:52:46: 3000000 INFO @ Tue, 02 Aug 2022 11:52:52: 8000000 INFO @ Tue, 02 Aug 2022 11:52:54: 7000000 INFO @ Tue, 02 Aug 2022 11:53:01: 4000000 INFO @ Tue, 02 Aug 2022 11:53:05: 8000000 INFO @ Tue, 02 Aug 2022 11:53:07: 9000000 INFO @ Tue, 02 Aug 2022 11:53:16: 9000000 INFO @ Tue, 02 Aug 2022 11:53:16: 5000000 INFO @ Tue, 02 Aug 2022 11:53:22: 10000000 INFO @ Tue, 02 Aug 2022 11:53:26: 10000000 INFO @ Tue, 02 Aug 2022 11:53:31: 6000000 INFO @ Tue, 02 Aug 2022 11:53:36: 11000000 INFO @ Tue, 02 Aug 2022 11:53:36: 11000000 INFO @ Tue, 02 Aug 2022 11:53:46: 7000000 INFO @ Tue, 02 Aug 2022 11:53:46: 12000000 INFO @ Tue, 02 Aug 2022 11:53:51: 12000000 INFO @ Tue, 02 Aug 2022 11:53:56: 13000000 INFO @ Tue, 02 Aug 2022 11:54:01: 8000000 INFO @ Tue, 02 Aug 2022 11:54:05: 13000000 INFO @ Tue, 02 Aug 2022 11:54:05: 14000000 INFO @ Tue, 02 Aug 2022 11:54:15: 15000000 INFO @ Tue, 02 Aug 2022 11:54:16: 9000000 INFO @ Tue, 02 Aug 2022 11:54:20: 14000000 INFO @ Tue, 02 Aug 2022 11:54:25: 16000000 INFO @ Tue, 02 Aug 2022 11:54:29: 10000000 INFO @ Tue, 02 Aug 2022 11:54:33: 15000000 INFO @ Tue, 02 Aug 2022 11:54:36: 17000000 INFO @ Tue, 02 Aug 2022 11:54:41: 11000000 INFO @ Tue, 02 Aug 2022 11:54:46: 18000000 INFO @ Tue, 02 Aug 2022 11:54:47: 16000000 INFO @ Tue, 02 Aug 2022 11:54:53: 12000000 INFO @ Tue, 02 Aug 2022 11:54:56: 19000000 INFO @ Tue, 02 Aug 2022 11:55:01: 17000000 INFO @ Tue, 02 Aug 2022 11:55:05: 13000000 INFO @ Tue, 02 Aug 2022 11:55:07: 20000000 INFO @ Tue, 02 Aug 2022 11:55:15: 18000000 INFO @ Tue, 02 Aug 2022 11:55:18: 14000000 INFO @ Tue, 02 Aug 2022 11:55:18: 21000000 INFO @ Tue, 02 Aug 2022 11:55:29: 22000000 INFO @ Tue, 02 Aug 2022 11:55:30: 15000000 INFO @ Tue, 02 Aug 2022 11:55:30: 19000000 INFO @ Tue, 02 Aug 2022 11:55:41: 23000000 INFO @ Tue, 02 Aug 2022 11:55:42: 16000000 INFO @ Tue, 02 Aug 2022 11:55:45: 20000000 INFO @ Tue, 02 Aug 2022 11:55:52: 24000000 INFO @ Tue, 02 Aug 2022 11:55:56: 17000000 INFO @ Tue, 02 Aug 2022 11:56:00: 21000000 INFO @ Tue, 02 Aug 2022 11:56:03: 25000000 INFO @ Tue, 02 Aug 2022 11:56:08: 18000000 INFO @ Tue, 02 Aug 2022 11:56:14: 26000000 INFO @ Tue, 02 Aug 2022 11:56:15: 22000000 INFO @ Tue, 02 Aug 2022 11:56:21: 19000000 INFO @ Tue, 02 Aug 2022 11:56:24: 27000000 INFO @ Tue, 02 Aug 2022 11:56:30: 23000000 INFO @ Tue, 02 Aug 2022 11:56:33: 20000000 INFO @ Tue, 02 Aug 2022 11:56:35: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:56:44: 24000000 INFO @ Tue, 02 Aug 2022 11:56:46: 29000000 INFO @ Tue, 02 Aug 2022 11:56:46: 21000000 INFO @ Tue, 02 Aug 2022 11:56:56: 30000000 INFO @ Tue, 02 Aug 2022 11:56:59: 25000000 INFO @ Tue, 02 Aug 2022 11:56:59: 22000000 INFO @ Tue, 02 Aug 2022 11:57:07: 31000000 INFO @ Tue, 02 Aug 2022 11:57:12: 23000000 INFO @ Tue, 02 Aug 2022 11:57:13: 26000000 INFO @ Tue, 02 Aug 2022 11:57:18: 32000000 INFO @ Tue, 02 Aug 2022 11:57:25: 24000000 INFO @ Tue, 02 Aug 2022 11:57:27: 27000000 INFO @ Tue, 02 Aug 2022 11:57:29: 33000000 INFO @ Tue, 02 Aug 2022 11:57:38: 25000000 INFO @ Tue, 02 Aug 2022 11:57:40: 34000000 INFO @ Tue, 02 Aug 2022 11:57:42: 28000000 INFO @ Tue, 02 Aug 2022 11:57:50: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:57:50: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:57:50: #1 total tags in treatment: 12516967 INFO @ Tue, 02 Aug 2022 11:57:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:57:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:57:51: #1 tags after filtering in treatment: 11463941 INFO @ Tue, 02 Aug 2022 11:57:51: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:57:51: #1 finished! INFO @ Tue, 02 Aug 2022 11:57:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:57:51: 26000000 INFO @ Tue, 02 Aug 2022 11:57:51: #2 number of paired peaks: 429 WARNING @ Tue, 02 Aug 2022 11:57:51: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 02 Aug 2022 11:57:51: start model_add_line... INFO @ Tue, 02 Aug 2022 11:57:52: start X-correlation... INFO @ Tue, 02 Aug 2022 11:57:52: end of X-cor INFO @ Tue, 02 Aug 2022 11:57:52: #2 finished! INFO @ Tue, 02 Aug 2022 11:57:52: #2 predicted fragment length is 220 bps INFO @ Tue, 02 Aug 2022 11:57:52: #2 alternative fragment length(s) may be 220 bps INFO @ Tue, 02 Aug 2022 11:57:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.10_model.r WARNING @ Tue, 02 Aug 2022 11:57:52: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:57:52: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Tue, 02 Aug 2022 11:57:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:57:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:57:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:57:56: 29000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:58:04: 27000000 INFO @ Tue, 02 Aug 2022 11:58:12: 30000000 INFO @ Tue, 02 Aug 2022 11:58:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:58:18: 28000000 INFO @ Tue, 02 Aug 2022 11:58:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:58:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:58:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.10_summits.bed INFO @ Tue, 02 Aug 2022 11:58:26: Done! INFO @ Tue, 02 Aug 2022 11:58:26: 31000000 pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (376 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:58:31: 29000000 INFO @ Tue, 02 Aug 2022 11:58:41: 32000000 INFO @ Tue, 02 Aug 2022 11:58:44: 30000000 INFO @ Tue, 02 Aug 2022 11:58:56: 33000000 INFO @ Tue, 02 Aug 2022 11:58:57: 31000000 INFO @ Tue, 02 Aug 2022 11:59:10: 34000000 INFO @ Tue, 02 Aug 2022 11:59:10: 32000000 INFO @ Tue, 02 Aug 2022 11:59:23: 33000000 INFO @ Tue, 02 Aug 2022 11:59:24: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:59:24: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:59:24: #1 total tags in treatment: 12516967 INFO @ Tue, 02 Aug 2022 11:59:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:59:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:59:24: #1 tags after filtering in treatment: 11463941 INFO @ Tue, 02 Aug 2022 11:59:24: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:59:24: #1 finished! INFO @ Tue, 02 Aug 2022 11:59:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:59:25: #2 number of paired peaks: 429 WARNING @ Tue, 02 Aug 2022 11:59:25: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 02 Aug 2022 11:59:25: start model_add_line... INFO @ Tue, 02 Aug 2022 11:59:25: start X-correlation... INFO @ Tue, 02 Aug 2022 11:59:25: end of X-cor INFO @ Tue, 02 Aug 2022 11:59:25: #2 finished! INFO @ Tue, 02 Aug 2022 11:59:25: #2 predicted fragment length is 220 bps INFO @ Tue, 02 Aug 2022 11:59:25: #2 alternative fragment length(s) may be 220 bps INFO @ Tue, 02 Aug 2022 11:59:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.05_model.r WARNING @ Tue, 02 Aug 2022 11:59:25: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:59:25: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Tue, 02 Aug 2022 11:59:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:59:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:59:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:59:36: 34000000 INFO @ Tue, 02 Aug 2022 11:59:48: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:59:48: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:59:48: #1 total tags in treatment: 12516967 INFO @ Tue, 02 Aug 2022 11:59:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:59:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:59:48: #1 tags after filtering in treatment: 11463941 INFO @ Tue, 02 Aug 2022 11:59:48: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:59:48: #1 finished! INFO @ Tue, 02 Aug 2022 11:59:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:59:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:59:49: #2 number of paired peaks: 429 WARNING @ Tue, 02 Aug 2022 11:59:50: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 02 Aug 2022 11:59:50: start model_add_line... INFO @ Tue, 02 Aug 2022 11:59:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:59:50: start X-correlation... INFO @ Tue, 02 Aug 2022 11:59:50: end of X-cor INFO @ Tue, 02 Aug 2022 11:59:50: #2 finished! INFO @ Tue, 02 Aug 2022 11:59:50: #2 predicted fragment length is 220 bps INFO @ Tue, 02 Aug 2022 11:59:50: #2 alternative fragment length(s) may be 220 bps INFO @ Tue, 02 Aug 2022 11:59:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.20_model.r WARNING @ Tue, 02 Aug 2022 11:59:50: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:59:50: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Tue, 02 Aug 2022 11:59:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:59:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:59:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:00:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:00:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:00:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.05_summits.bed INFO @ Tue, 02 Aug 2022 12:00:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 164 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:00:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:00:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:00:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:00:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336913/SRX13336913.20_summits.bed INFO @ Tue, 02 Aug 2022 12:00:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (279 records, 4 fields): 23 millis CompletedMACS2peakCalling