Job ID = 16432481 SRX = SRX15407790 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:32:24 prefetch.2.10.7: 1) Downloading 'SRR19348961'... 2022-08-02T00:32:24 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:33:06 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:33:08 prefetch.2.10.7: 'SRR19348961' is valid 2022-08-02T00:33:08 prefetch.2.10.7: 1) 'SRR19348961' was downloaded successfully 2022-08-02T00:33:08 prefetch.2.10.7: 'SRR19348961' has 0 unresolved dependencies Read 17496603 spots for SRR19348961/SRR19348961.sra Written 17496603 spots for SRR19348961/SRR19348961.sra fastq に変換しました。 bowtie でマッピング中... Your job 16433870 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:51 17496603 reads; of these: 17496603 (100.00%) were unpaired; of these: 393863 (2.25%) aligned 0 times 14591188 (83.39%) aligned exactly 1 time 2511552 (14.35%) aligned >1 times 97.75% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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 8 files... [bam_rmdupse_core] 1703384 / 17102740 = 0.0996 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 09:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.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 09:47:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:47:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:47:22: 1000000 INFO @ Tue, 02 Aug 2022 09:47:32: 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 09:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.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 09:47:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:47:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:47:43: 3000000 INFO @ Tue, 02 Aug 2022 09:47:51: 1000000 INFO @ Tue, 02 Aug 2022 09:47:53: 4000000 INFO @ Tue, 02 Aug 2022 09:48:00: 2000000 INFO @ Tue, 02 Aug 2022 09:48:04: 5000000 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 09:48:10: 3000000 INFO @ Tue, 02 Aug 2022 09:48:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.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 09:48:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:48:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:48:14: 6000000 INFO @ Tue, 02 Aug 2022 09:48:20: 4000000 INFO @ Tue, 02 Aug 2022 09:48:21: 1000000 INFO @ Tue, 02 Aug 2022 09:48:25: 7000000 INFO @ Tue, 02 Aug 2022 09:48:30: 5000000 INFO @ Tue, 02 Aug 2022 09:48:31: 2000000 INFO @ Tue, 02 Aug 2022 09:48:35: 8000000 INFO @ Tue, 02 Aug 2022 09:48:39: 6000000 INFO @ Tue, 02 Aug 2022 09:48:41: 3000000 INFO @ Tue, 02 Aug 2022 09:48:46: 9000000 INFO @ Tue, 02 Aug 2022 09:48:49: 7000000 INFO @ Tue, 02 Aug 2022 09:48:51: 4000000 INFO @ Tue, 02 Aug 2022 09:48:56: 10000000 INFO @ Tue, 02 Aug 2022 09:48:59: 8000000 INFO @ Tue, 02 Aug 2022 09:49:01: 5000000 INFO @ Tue, 02 Aug 2022 09:49:06: 11000000 INFO @ Tue, 02 Aug 2022 09:49:09: 9000000 INFO @ Tue, 02 Aug 2022 09:49:11: 6000000 INFO @ Tue, 02 Aug 2022 09:49:17: 12000000 INFO @ Tue, 02 Aug 2022 09:49:19: 10000000 INFO @ Tue, 02 Aug 2022 09:49:21: 7000000 INFO @ Tue, 02 Aug 2022 09:49:27: 13000000 INFO @ Tue, 02 Aug 2022 09:49:29: 11000000 INFO @ Tue, 02 Aug 2022 09:49:30: 8000000 INFO @ Tue, 02 Aug 2022 09:49:38: 14000000 INFO @ Tue, 02 Aug 2022 09:49:39: 12000000 INFO @ Tue, 02 Aug 2022 09:49:40: 9000000 INFO @ Tue, 02 Aug 2022 09:49:48: 15000000 INFO @ Tue, 02 Aug 2022 09:49:50: 13000000 INFO @ Tue, 02 Aug 2022 09:49:50: 10000000 INFO @ Tue, 02 Aug 2022 09:49:52: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:49:52: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:49:52: #1 total tags in treatment: 15399356 INFO @ Tue, 02 Aug 2022 09:49:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:49:52: #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 09:49:53: #1 tags after filtering in treatment: 15399356 INFO @ Tue, 02 Aug 2022 09:49:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:49:53: #1 finished! INFO @ Tue, 02 Aug 2022 09:49:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:49:53: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:49:54: #2 number of paired peaks: 184 WARNING @ Tue, 02 Aug 2022 09:49:54: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 02 Aug 2022 09:49:54: start model_add_line... INFO @ Tue, 02 Aug 2022 09:49:54: start X-correlation... INFO @ Tue, 02 Aug 2022 09:49:54: end of X-cor INFO @ Tue, 02 Aug 2022 09:49:54: #2 finished! INFO @ Tue, 02 Aug 2022 09:49:54: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 09:49:54: #2 alternative fragment length(s) may be 2,72,595 bps INFO @ Tue, 02 Aug 2022 09:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.05_model.r WARNING @ Tue, 02 Aug 2022 09:49:54: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:49:54: #2 You may need to consider one of the other alternative d(s): 2,72,595 WARNING @ Tue, 02 Aug 2022 09:49:54: #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 09:49:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:50:00: 14000000 INFO @ Tue, 02 Aug 2022 09:50:00: 11000000 INFO @ Tue, 02 Aug 2022 09:50:10: 15000000 INFO @ Tue, 02 Aug 2022 09:50:10: 12000000 INFO @ Tue, 02 Aug 2022 09:50:13: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:50:13: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:50:13: #1 total tags in treatment: 15399356 INFO @ Tue, 02 Aug 2022 09:50:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:50:13: #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 09:50:14: #1 tags after filtering in treatment: 15399356 INFO @ Tue, 02 Aug 2022 09:50:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:50:14: #1 finished! INFO @ Tue, 02 Aug 2022 09:50:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:50:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:50:15: #2 number of paired peaks: 184 WARNING @ Tue, 02 Aug 2022 09:50:15: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 02 Aug 2022 09:50:15: start model_add_line... INFO @ Tue, 02 Aug 2022 09:50:15: start X-correlation... INFO @ Tue, 02 Aug 2022 09:50:15: end of X-cor INFO @ Tue, 02 Aug 2022 09:50:15: #2 finished! INFO @ Tue, 02 Aug 2022 09:50:15: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 09:50:15: #2 alternative fragment length(s) may be 2,72,595 bps INFO @ Tue, 02 Aug 2022 09:50:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.10_model.r WARNING @ Tue, 02 Aug 2022 09:50:15: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:50:15: #2 You may need to consider one of the other alternative d(s): 2,72,595 WARNING @ Tue, 02 Aug 2022 09:50:15: #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 09:50:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:50:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:50:20: 13000000 INFO @ Tue, 02 Aug 2022 09:50:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:50:29: 14000000 INFO @ Tue, 02 Aug 2022 09:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.05_summits.bed INFO @ Tue, 02 Aug 2022 09:50:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (565 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:50:39: 15000000 INFO @ Tue, 02 Aug 2022 09:50:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:50:43: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:50:43: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:50:43: #1 total tags in treatment: 15399356 INFO @ Tue, 02 Aug 2022 09:50:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:50:43: #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 09:50:43: #1 tags after filtering in treatment: 15399356 INFO @ Tue, 02 Aug 2022 09:50:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:50:43: #1 finished! INFO @ Tue, 02 Aug 2022 09:50:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:50:43: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:50:44: #2 number of paired peaks: 184 WARNING @ Tue, 02 Aug 2022 09:50:44: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 02 Aug 2022 09:50:44: start model_add_line... INFO @ Tue, 02 Aug 2022 09:50:44: start X-correlation... INFO @ Tue, 02 Aug 2022 09:50:44: end of X-cor INFO @ Tue, 02 Aug 2022 09:50:44: #2 finished! INFO @ Tue, 02 Aug 2022 09:50:44: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 09:50:44: #2 alternative fragment length(s) may be 2,72,595 bps INFO @ Tue, 02 Aug 2022 09:50:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.20_model.r WARNING @ Tue, 02 Aug 2022 09:50:44: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:50:44: #2 You may need to consider one of the other alternative d(s): 2,72,595 WARNING @ Tue, 02 Aug 2022 09:50:44: #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 09:50:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:50:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:50:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:50:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:50:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.10_summits.bed INFO @ Tue, 02 Aug 2022 09:50:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:51:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:51:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:51:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:51:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407790/SRX15407790.20_summits.bed INFO @ Tue, 02 Aug 2022 09:51:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 39 millis CompletedMACS2peakCalling