Job ID = 14159621 SRX = SRX3180785 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11621086 spots for SRR6030436/SRR6030436.sra Written 11621086 spots for SRR6030436/SRR6030436.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160125 ("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: 00:02:47 11621086 reads; of these: 11621086 (100.00%) were unpaired; of these: 452338 (3.89%) aligned 0 times 9033203 (77.73%) aligned exactly 1 time 2135545 (18.38%) aligned >1 times 96.11% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 1216152 / 11168748 = 0.1089 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 23:34:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.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 23:34:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:34:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:34:40: 1000000 INFO @ Wed, 08 Dec 2021 23:34:44: 2000000 INFO @ Wed, 08 Dec 2021 23:34:49: 3000000 INFO @ Wed, 08 Dec 2021 23:34:54: 4000000 INFO @ Wed, 08 Dec 2021 23:34:59: 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 23:35:04: 6000000 INFO @ Wed, 08 Dec 2021 23:35:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.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 23:35:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:35:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:35:08: 7000000 INFO @ Wed, 08 Dec 2021 23:35:11: 1000000 INFO @ Wed, 08 Dec 2021 23:35:13: 8000000 INFO @ Wed, 08 Dec 2021 23:35:16: 2000000 INFO @ Wed, 08 Dec 2021 23:35:18: 9000000 INFO @ Wed, 08 Dec 2021 23:35:22: 3000000 INFO @ Wed, 08 Dec 2021 23:35:23: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:35:23: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:35:23: #1 total tags in treatment: 9952596 INFO @ Wed, 08 Dec 2021 23:35:23: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:35:23: #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 23:35:23: #1 tags after filtering in treatment: 9952596 INFO @ Wed, 08 Dec 2021 23:35:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:35:23: #1 finished! INFO @ Wed, 08 Dec 2021 23:35:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:35:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:35:24: #2 number of paired peaks: 395 WARNING @ Wed, 08 Dec 2021 23:35:24: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Wed, 08 Dec 2021 23:35:24: start model_add_line... INFO @ Wed, 08 Dec 2021 23:35:24: start X-correlation... INFO @ Wed, 08 Dec 2021 23:35:24: end of X-cor INFO @ Wed, 08 Dec 2021 23:35:24: #2 finished! INFO @ Wed, 08 Dec 2021 23:35:24: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:35:24: #2 alternative fragment length(s) may be 3,48,566 bps INFO @ Wed, 08 Dec 2021 23:35:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.05_model.r WARNING @ Wed, 08 Dec 2021 23:35:24: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:35:24: #2 You may need to consider one of the other alternative d(s): 3,48,566 WARNING @ Wed, 08 Dec 2021 23:35:24: #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 23:35:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:35:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:35:28: 4000000 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 23:35:33: 5000000 INFO @ Wed, 08 Dec 2021 23:35:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.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 23:35:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:35:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:35:39: 6000000 INFO @ Wed, 08 Dec 2021 23:35:40: 1000000 INFO @ Wed, 08 Dec 2021 23:35:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:35:44: 7000000 INFO @ Wed, 08 Dec 2021 23:35:45: 2000000 INFO @ Wed, 08 Dec 2021 23:35:50: 3000000 INFO @ Wed, 08 Dec 2021 23:35:50: 8000000 INFO @ Wed, 08 Dec 2021 23:35:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:35:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:35:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.05_summits.bed INFO @ Wed, 08 Dec 2021 23:35:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (655 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:35:55: 4000000 INFO @ Wed, 08 Dec 2021 23:35:55: 9000000 INFO @ Wed, 08 Dec 2021 23:36:00: 5000000 INFO @ Wed, 08 Dec 2021 23:36:01: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:36:01: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:36:01: #1 total tags in treatment: 9952596 INFO @ Wed, 08 Dec 2021 23:36:01: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:36:01: #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 23:36:01: #1 tags after filtering in treatment: 9952596 INFO @ Wed, 08 Dec 2021 23:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:36:01: #1 finished! INFO @ Wed, 08 Dec 2021 23:36:01: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:36:02: #2 number of paired peaks: 395 WARNING @ Wed, 08 Dec 2021 23:36:02: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Wed, 08 Dec 2021 23:36:02: start model_add_line... INFO @ Wed, 08 Dec 2021 23:36:02: start X-correlation... INFO @ Wed, 08 Dec 2021 23:36:02: end of X-cor INFO @ Wed, 08 Dec 2021 23:36:02: #2 finished! INFO @ Wed, 08 Dec 2021 23:36:02: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:36:02: #2 alternative fragment length(s) may be 3,48,566 bps INFO @ Wed, 08 Dec 2021 23:36:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.10_model.r WARNING @ Wed, 08 Dec 2021 23:36:02: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:36:02: #2 You may need to consider one of the other alternative d(s): 3,48,566 WARNING @ Wed, 08 Dec 2021 23:36:02: #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 23:36:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:36:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:36:05: 6000000 INFO @ Wed, 08 Dec 2021 23:36:09: 7000000 INFO @ Wed, 08 Dec 2021 23:36:14: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:36:19: 9000000 INFO @ Wed, 08 Dec 2021 23:36:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:36:24: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:36:24: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:36:24: #1 total tags in treatment: 9952596 INFO @ Wed, 08 Dec 2021 23:36:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:36:24: #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 23:36:24: #1 tags after filtering in treatment: 9952596 INFO @ Wed, 08 Dec 2021 23:36:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:36:24: #1 finished! INFO @ Wed, 08 Dec 2021 23:36:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:36:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:36:24: #2 number of paired peaks: 395 WARNING @ Wed, 08 Dec 2021 23:36:24: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Wed, 08 Dec 2021 23:36:24: start model_add_line... INFO @ Wed, 08 Dec 2021 23:36:25: start X-correlation... INFO @ Wed, 08 Dec 2021 23:36:25: end of X-cor INFO @ Wed, 08 Dec 2021 23:36:25: #2 finished! INFO @ Wed, 08 Dec 2021 23:36:25: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:36:25: #2 alternative fragment length(s) may be 3,48,566 bps INFO @ Wed, 08 Dec 2021 23:36:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.20_model.r WARNING @ Wed, 08 Dec 2021 23:36:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:36:25: #2 You may need to consider one of the other alternative d(s): 3,48,566 WARNING @ Wed, 08 Dec 2021 23:36:25: #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 23:36:25: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:36:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.10_summits.bed INFO @ Wed, 08 Dec 2021 23:36:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:36:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:36:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:36:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:36:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180785/SRX3180785.20_summits.bed INFO @ Wed, 08 Dec 2021 23:36:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (205 records, 4 fields): 2 millis CompletedMACS2peakCalling