Job ID = 14157868 SRX = SRX6799186 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 35279189 spots for SRR10065393/SRR10065393.sra Written 35279189 spots for SRR10065393/SRR10065393.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158040 ("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: 00:08:20 35279189 reads; of these: 35279189 (100.00%) were unpaired; of these: 1633576 (4.63%) aligned 0 times 26488531 (75.08%) aligned exactly 1 time 7157082 (20.29%) aligned >1 times 95.37% overall alignment rate Time searching: 00:08:20 Overall time: 00:08:20 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_rmdupse_core] 9685316 / 33645613 = 0.2879 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:05:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.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 @ Wed, 08 Dec 2021 12:05:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:05:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:05:37: 1000000 INFO @ Wed, 08 Dec 2021 12:05:41: 2000000 INFO @ Wed, 08 Dec 2021 12:05:46: 3000000 INFO @ Wed, 08 Dec 2021 12:05:51: 4000000 INFO @ Wed, 08 Dec 2021 12:05:56: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:06:01: 6000000 INFO @ Wed, 08 Dec 2021 12:06:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.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 @ Wed, 08 Dec 2021 12:06:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:06:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:06:07: 7000000 INFO @ Wed, 08 Dec 2021 12:06:07: 1000000 INFO @ Wed, 08 Dec 2021 12:06:12: 8000000 INFO @ Wed, 08 Dec 2021 12:06:14: 2000000 INFO @ Wed, 08 Dec 2021 12:06:18: 9000000 INFO @ Wed, 08 Dec 2021 12:06:20: 3000000 INFO @ Wed, 08 Dec 2021 12:06:23: 10000000 INFO @ Wed, 08 Dec 2021 12:06:26: 4000000 INFO @ Wed, 08 Dec 2021 12:06:29: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.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 @ Wed, 08 Dec 2021 12:06:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:06:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:06:32: 5000000 INFO @ Wed, 08 Dec 2021 12:06:35: 12000000 INFO @ Wed, 08 Dec 2021 12:06:37: 1000000 INFO @ Wed, 08 Dec 2021 12:06:38: 6000000 INFO @ Wed, 08 Dec 2021 12:06:40: 13000000 INFO @ Wed, 08 Dec 2021 12:06:43: 2000000 INFO @ Wed, 08 Dec 2021 12:06:44: 7000000 INFO @ Wed, 08 Dec 2021 12:06:46: 14000000 INFO @ Wed, 08 Dec 2021 12:06:48: 3000000 INFO @ Wed, 08 Dec 2021 12:06:50: 8000000 INFO @ Wed, 08 Dec 2021 12:06:51: 15000000 INFO @ Wed, 08 Dec 2021 12:06:54: 4000000 INFO @ Wed, 08 Dec 2021 12:06:56: 9000000 INFO @ Wed, 08 Dec 2021 12:06:57: 16000000 INFO @ Wed, 08 Dec 2021 12:06:59: 5000000 INFO @ Wed, 08 Dec 2021 12:07:02: 10000000 INFO @ Wed, 08 Dec 2021 12:07:02: 17000000 INFO @ Wed, 08 Dec 2021 12:07:05: 6000000 INFO @ Wed, 08 Dec 2021 12:07:08: 18000000 INFO @ Wed, 08 Dec 2021 12:07:08: 11000000 INFO @ Wed, 08 Dec 2021 12:07:11: 7000000 INFO @ Wed, 08 Dec 2021 12:07:13: 19000000 INFO @ Wed, 08 Dec 2021 12:07:15: 12000000 INFO @ Wed, 08 Dec 2021 12:07:16: 8000000 INFO @ Wed, 08 Dec 2021 12:07:19: 20000000 INFO @ Wed, 08 Dec 2021 12:07:21: 13000000 INFO @ Wed, 08 Dec 2021 12:07:22: 9000000 INFO @ Wed, 08 Dec 2021 12:07:24: 21000000 INFO @ Wed, 08 Dec 2021 12:07:27: 14000000 INFO @ Wed, 08 Dec 2021 12:07:27: 10000000 INFO @ Wed, 08 Dec 2021 12:07:30: 22000000 INFO @ Wed, 08 Dec 2021 12:07:33: 11000000 INFO @ Wed, 08 Dec 2021 12:07:33: 15000000 INFO @ Wed, 08 Dec 2021 12:07:35: 23000000 INFO @ Wed, 08 Dec 2021 12:07:38: 12000000 INFO @ Wed, 08 Dec 2021 12:07:39: 16000000 INFO @ Wed, 08 Dec 2021 12:07:41: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:07:41: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:07:41: #1 total tags in treatment: 23960297 INFO @ Wed, 08 Dec 2021 12:07:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:07:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:07:41: #1 tags after filtering in treatment: 23960297 INFO @ Wed, 08 Dec 2021 12:07:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:07:41: #1 finished! INFO @ Wed, 08 Dec 2021 12:07:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:07:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:07:42: #2 number of paired peaks: 159 WARNING @ Wed, 08 Dec 2021 12:07:42: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Wed, 08 Dec 2021 12:07:42: start model_add_line... INFO @ Wed, 08 Dec 2021 12:07:43: start X-correlation... INFO @ Wed, 08 Dec 2021 12:07:43: end of X-cor INFO @ Wed, 08 Dec 2021 12:07:43: #2 finished! INFO @ Wed, 08 Dec 2021 12:07:43: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 12:07:43: #2 alternative fragment length(s) may be 3,52,118,198 bps INFO @ Wed, 08 Dec 2021 12:07:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05_model.r WARNING @ Wed, 08 Dec 2021 12:07:43: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:07:43: #2 You may need to consider one of the other alternative d(s): 3,52,118,198 WARNING @ Wed, 08 Dec 2021 12:07:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:07:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:07:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:07:44: 13000000 INFO @ Wed, 08 Dec 2021 12:07:45: 17000000 INFO @ Wed, 08 Dec 2021 12:07:49: 14000000 INFO @ Wed, 08 Dec 2021 12:07:51: 18000000 INFO @ Wed, 08 Dec 2021 12:07:54: 15000000 INFO @ Wed, 08 Dec 2021 12:07:57: 19000000 INFO @ Wed, 08 Dec 2021 12:08:00: 16000000 INFO @ Wed, 08 Dec 2021 12:08:03: 20000000 INFO @ Wed, 08 Dec 2021 12:08:05: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:08:09: 21000000 INFO @ Wed, 08 Dec 2021 12:08:11: 18000000 INFO @ Wed, 08 Dec 2021 12:08:15: 22000000 INFO @ Wed, 08 Dec 2021 12:08:16: 19000000 INFO @ Wed, 08 Dec 2021 12:08:21: 23000000 INFO @ Wed, 08 Dec 2021 12:08:21: 20000000 INFO @ Wed, 08 Dec 2021 12:08:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:08:27: 21000000 INFO @ Wed, 08 Dec 2021 12:08:27: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:08:27: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:08:27: #1 total tags in treatment: 23960297 INFO @ Wed, 08 Dec 2021 12:08:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:08:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:08:27: #1 tags after filtering in treatment: 23960297 INFO @ Wed, 08 Dec 2021 12:08:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:08:27: #1 finished! INFO @ Wed, 08 Dec 2021 12:08:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:08:29: #2 number of paired peaks: 159 WARNING @ Wed, 08 Dec 2021 12:08:29: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Wed, 08 Dec 2021 12:08:29: start model_add_line... INFO @ Wed, 08 Dec 2021 12:08:29: start X-correlation... INFO @ Wed, 08 Dec 2021 12:08:29: end of X-cor INFO @ Wed, 08 Dec 2021 12:08:29: #2 finished! INFO @ Wed, 08 Dec 2021 12:08:29: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 12:08:29: #2 alternative fragment length(s) may be 3,52,118,198 bps INFO @ Wed, 08 Dec 2021 12:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10_model.r WARNING @ Wed, 08 Dec 2021 12:08:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:08:29: #2 You may need to consider one of the other alternative d(s): 3,52,118,198 WARNING @ Wed, 08 Dec 2021 12:08:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:08:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:08:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:08:32: 22000000 INFO @ Wed, 08 Dec 2021 12:08:37: 23000000 INFO @ Wed, 08 Dec 2021 12:08:42: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:08:42: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:08:42: #1 total tags in treatment: 23960297 INFO @ Wed, 08 Dec 2021 12:08:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:08:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:08:42: #1 tags after filtering in treatment: 23960297 INFO @ Wed, 08 Dec 2021 12:08:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:08:42: #1 finished! INFO @ Wed, 08 Dec 2021 12:08:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:08:43: #2 number of paired peaks: 159 WARNING @ Wed, 08 Dec 2021 12:08:43: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Wed, 08 Dec 2021 12:08:43: start model_add_line... INFO @ Wed, 08 Dec 2021 12:08:44: start X-correlation... INFO @ Wed, 08 Dec 2021 12:08:44: end of X-cor INFO @ Wed, 08 Dec 2021 12:08:44: #2 finished! INFO @ Wed, 08 Dec 2021 12:08:44: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 12:08:44: #2 alternative fragment length(s) may be 3,52,118,198 bps INFO @ Wed, 08 Dec 2021 12:08:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20_model.r WARNING @ Wed, 08 Dec 2021 12:08:44: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:08:44: #2 You may need to consider one of the other alternative d(s): 3,52,118,198 WARNING @ Wed, 08 Dec 2021 12:08:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:08:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:08:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:08:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:08:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:08:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05_summits.bed INFO @ Wed, 08 Dec 2021 12:08:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9542 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:09:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:09:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:09:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:09:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:09:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10_summits.bed INFO @ Wed, 08 Dec 2021 12:09:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2698 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:09:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:09:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:09:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20_summits.bed INFO @ Wed, 08 Dec 2021 12:09:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (391 records, 4 fields): 2 millis CompletedMACS2peakCalling