Job ID = 14159231 SRX = SRX3180800 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16836975 spots for SRR6030451/SRR6030451.sra Written 16836975 spots for SRR6030451/SRR6030451.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159438 ("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: 00:03:31 16836975 reads; of these: 16836975 (100.00%) were unpaired; of these: 2246746 (13.34%) aligned 0 times 11630290 (69.08%) aligned exactly 1 time 2959939 (17.58%) aligned >1 times 86.66% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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] 4559701 / 14590229 = 0.3125 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 20:26:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.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 20:26:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:26:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:27:05: 1000000 INFO @ Wed, 08 Dec 2021 20:27:10: 2000000 INFO @ Wed, 08 Dec 2021 20:27:16: 3000000 INFO @ Wed, 08 Dec 2021 20:27:21: 4000000 INFO @ Wed, 08 Dec 2021 20:27:26: 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 20:27:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.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 20:27:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:27:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:27:32: 6000000 INFO @ Wed, 08 Dec 2021 20:27:34: 1000000 INFO @ Wed, 08 Dec 2021 20:27:38: 7000000 INFO @ Wed, 08 Dec 2021 20:27:40: 2000000 INFO @ Wed, 08 Dec 2021 20:27:44: 8000000 INFO @ Wed, 08 Dec 2021 20:27:46: 3000000 INFO @ Wed, 08 Dec 2021 20:27:50: 9000000 INFO @ Wed, 08 Dec 2021 20:27:52: 4000000 INFO @ Wed, 08 Dec 2021 20:27:56: 10000000 INFO @ Wed, 08 Dec 2021 20:27:56: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:27:56: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:27:56: #1 total tags in treatment: 10030528 INFO @ Wed, 08 Dec 2021 20:27:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:27:56: #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 20:27:56: #1 tags after filtering in treatment: 10030528 INFO @ Wed, 08 Dec 2021 20:27:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:27:56: #1 finished! INFO @ Wed, 08 Dec 2021 20:27:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:27:56: #2 looking for paired plus/minus strand peaks... 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 20:27:57: #2 number of paired peaks: 484 WARNING @ Wed, 08 Dec 2021 20:27:57: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Wed, 08 Dec 2021 20:27:57: start model_add_line... INFO @ Wed, 08 Dec 2021 20:27:57: start X-correlation... INFO @ Wed, 08 Dec 2021 20:27:57: end of X-cor INFO @ Wed, 08 Dec 2021 20:27:57: #2 finished! INFO @ Wed, 08 Dec 2021 20:27:57: #2 predicted fragment length is 44 bps INFO @ Wed, 08 Dec 2021 20:27:57: #2 alternative fragment length(s) may be 2,44 bps INFO @ Wed, 08 Dec 2021 20:27:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.05_model.r WARNING @ Wed, 08 Dec 2021 20:27:57: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:27:57: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Wed, 08 Dec 2021 20:27:57: #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 20:27:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:27:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:27:58: 5000000 INFO @ Wed, 08 Dec 2021 20:27:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.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 20:27:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:27:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:28:04: 6000000 INFO @ Wed, 08 Dec 2021 20:28:06: 1000000 INFO @ Wed, 08 Dec 2021 20:28:11: 7000000 INFO @ Wed, 08 Dec 2021 20:28:13: 2000000 INFO @ Wed, 08 Dec 2021 20:28:16: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:28:17: 8000000 INFO @ Wed, 08 Dec 2021 20:28:20: 3000000 INFO @ Wed, 08 Dec 2021 20:28:23: 9000000 INFO @ Wed, 08 Dec 2021 20:28:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:28:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:28:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.05_summits.bed INFO @ Wed, 08 Dec 2021 20:28:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:28:28: 4000000 INFO @ Wed, 08 Dec 2021 20:28:30: 10000000 INFO @ Wed, 08 Dec 2021 20:28:30: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:28:30: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:28:30: #1 total tags in treatment: 10030528 INFO @ Wed, 08 Dec 2021 20:28:30: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:28:30: #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 20:28:30: #1 tags after filtering in treatment: 10030528 INFO @ Wed, 08 Dec 2021 20:28:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:28:30: #1 finished! INFO @ Wed, 08 Dec 2021 20:28:30: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:28:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:28:31: #2 number of paired peaks: 484 WARNING @ Wed, 08 Dec 2021 20:28:31: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Wed, 08 Dec 2021 20:28:31: start model_add_line... INFO @ Wed, 08 Dec 2021 20:28:31: start X-correlation... INFO @ Wed, 08 Dec 2021 20:28:31: end of X-cor INFO @ Wed, 08 Dec 2021 20:28:31: #2 finished! INFO @ Wed, 08 Dec 2021 20:28:31: #2 predicted fragment length is 44 bps INFO @ Wed, 08 Dec 2021 20:28:31: #2 alternative fragment length(s) may be 2,44 bps INFO @ Wed, 08 Dec 2021 20:28:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.10_model.r WARNING @ Wed, 08 Dec 2021 20:28:31: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:28:31: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Wed, 08 Dec 2021 20:28:31: #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 20:28:31: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:28:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:28:35: 5000000 BedGraph に変換しました。 INFO @ Wed, 08 Dec 2021 20:28:41: 6000000 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:28:48: 7000000 INFO @ Wed, 08 Dec 2021 20:28:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:28:55: 8000000 INFO @ Wed, 08 Dec 2021 20:28:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:28:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:28:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.10_summits.bed INFO @ Wed, 08 Dec 2021 20:28:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (445 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:29:02: 9000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:29:09: 10000000 INFO @ Wed, 08 Dec 2021 20:29:09: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:29:09: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:29:09: #1 total tags in treatment: 10030528 INFO @ Wed, 08 Dec 2021 20:29:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:29:09: #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 20:29:09: #1 tags after filtering in treatment: 10030528 INFO @ Wed, 08 Dec 2021 20:29:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:29:09: #1 finished! INFO @ Wed, 08 Dec 2021 20:29:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:29:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:29:10: #2 number of paired peaks: 484 WARNING @ Wed, 08 Dec 2021 20:29:10: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Wed, 08 Dec 2021 20:29:10: start model_add_line... INFO @ Wed, 08 Dec 2021 20:29:10: start X-correlation... INFO @ Wed, 08 Dec 2021 20:29:10: end of X-cor INFO @ Wed, 08 Dec 2021 20:29:10: #2 finished! INFO @ Wed, 08 Dec 2021 20:29:10: #2 predicted fragment length is 44 bps INFO @ Wed, 08 Dec 2021 20:29:10: #2 alternative fragment length(s) may be 2,44 bps INFO @ Wed, 08 Dec 2021 20:29:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.20_model.r WARNING @ Wed, 08 Dec 2021 20:29:10: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:29:10: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Wed, 08 Dec 2021 20:29:10: #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 20:29:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:29:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:29:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:29:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:29:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:29:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180800/SRX3180800.20_summits.bed INFO @ Wed, 08 Dec 2021 20:29:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 2 millis CompletedMACS2peakCalling