Job ID = 14159585 SRX = SRX3180773 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12009636 spots for SRR6030424/SRR6030424.sra Written 12009636 spots for SRR6030424/SRR6030424.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159936 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:35 12009636 reads; of these: 12009636 (100.00%) were unpaired; of these: 769446 (6.41%) aligned 0 times 9042067 (75.29%) aligned exactly 1 time 2198123 (18.30%) aligned >1 times 93.59% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 4345634 / 11240190 = 0.3866 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 23:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.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 23:00:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:00:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:00:38: 1000000 INFO @ Wed, 08 Dec 2021 23:00:47: 2000000 INFO @ Wed, 08 Dec 2021 23:00:55: 3000000 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 23:00:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.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 23:00:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:00:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:01:05: 4000000 INFO @ Wed, 08 Dec 2021 23:01:09: 1000000 INFO @ Wed, 08 Dec 2021 23:01:15: 5000000 INFO @ Wed, 08 Dec 2021 23:01:18: 2000000 INFO @ Wed, 08 Dec 2021 23:01:24: 6000000 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 23:01:28: 3000000 INFO @ Wed, 08 Dec 2021 23:01:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.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 23:01:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:01:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:01:32: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:01:32: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:01:32: #1 total tags in treatment: 6894556 INFO @ Wed, 08 Dec 2021 23:01:32: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:01:32: #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 23:01:32: #1 tags after filtering in treatment: 6894556 INFO @ Wed, 08 Dec 2021 23:01:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:01:32: #1 finished! INFO @ Wed, 08 Dec 2021 23:01:32: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:01:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:01:33: #2 number of paired peaks: 519 WARNING @ Wed, 08 Dec 2021 23:01:33: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Wed, 08 Dec 2021 23:01:33: start model_add_line... INFO @ Wed, 08 Dec 2021 23:01:33: start X-correlation... INFO @ Wed, 08 Dec 2021 23:01:33: end of X-cor INFO @ Wed, 08 Dec 2021 23:01:33: #2 finished! INFO @ Wed, 08 Dec 2021 23:01:33: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:01:33: #2 alternative fragment length(s) may be 3,48,570 bps INFO @ Wed, 08 Dec 2021 23:01:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.05_model.r WARNING @ Wed, 08 Dec 2021 23:01:33: #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 23:01:33: #2 You may need to consider one of the other alternative d(s): 3,48,570 WARNING @ Wed, 08 Dec 2021 23:01:33: #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 23:01:33: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:01:37: 4000000 INFO @ Wed, 08 Dec 2021 23:01:39: 1000000 INFO @ Wed, 08 Dec 2021 23:01:46: 5000000 INFO @ Wed, 08 Dec 2021 23:01:48: 2000000 INFO @ Wed, 08 Dec 2021 23:01:55: 6000000 INFO @ Wed, 08 Dec 2021 23:01:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:01:57: 3000000 INFO @ Wed, 08 Dec 2021 23:02:03: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:02:03: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:02:03: #1 total tags in treatment: 6894556 INFO @ Wed, 08 Dec 2021 23:02:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:02:03: #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 23:02:03: #1 tags after filtering in treatment: 6894556 INFO @ Wed, 08 Dec 2021 23:02:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:02:03: #1 finished! INFO @ Wed, 08 Dec 2021 23:02:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:02:04: #2 number of paired peaks: 519 WARNING @ Wed, 08 Dec 2021 23:02:04: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Wed, 08 Dec 2021 23:02:04: start model_add_line... INFO @ Wed, 08 Dec 2021 23:02:04: start X-correlation... INFO @ Wed, 08 Dec 2021 23:02:04: end of X-cor INFO @ Wed, 08 Dec 2021 23:02:04: #2 finished! INFO @ Wed, 08 Dec 2021 23:02:04: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:02:04: #2 alternative fragment length(s) may be 3,48,570 bps INFO @ Wed, 08 Dec 2021 23:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.10_model.r WARNING @ Wed, 08 Dec 2021 23:02:04: #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 23:02:04: #2 You may need to consider one of the other alternative d(s): 3,48,570 WARNING @ Wed, 08 Dec 2021 23:02:04: #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 23:02:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:02:05: 4000000 INFO @ Wed, 08 Dec 2021 23:02:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:02:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:02:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.05_summits.bed INFO @ Wed, 08 Dec 2021 23:02:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (686 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:02:13: 5000000 INFO @ Wed, 08 Dec 2021 23:02:21: 6000000 INFO @ Wed, 08 Dec 2021 23:02:25: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:02:29: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:02:29: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:02:29: #1 total tags in treatment: 6894556 INFO @ Wed, 08 Dec 2021 23:02:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:02:29: #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 23:02:29: #1 tags after filtering in treatment: 6894556 INFO @ Wed, 08 Dec 2021 23:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:02:29: #1 finished! INFO @ Wed, 08 Dec 2021 23:02:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:02:30: #2 number of paired peaks: 519 WARNING @ Wed, 08 Dec 2021 23:02:30: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Wed, 08 Dec 2021 23:02:30: start model_add_line... INFO @ Wed, 08 Dec 2021 23:02:30: start X-correlation... INFO @ Wed, 08 Dec 2021 23:02:30: end of X-cor INFO @ Wed, 08 Dec 2021 23:02:30: #2 finished! INFO @ Wed, 08 Dec 2021 23:02:30: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:02:30: #2 alternative fragment length(s) may be 3,48,570 bps INFO @ Wed, 08 Dec 2021 23:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.20_model.r WARNING @ Wed, 08 Dec 2021 23:02:30: #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 23:02:30: #2 You may need to consider one of the other alternative d(s): 3,48,570 WARNING @ Wed, 08 Dec 2021 23:02:30: #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 23:02:30: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:02:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:02:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:02:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.10_summits.bed INFO @ Wed, 08 Dec 2021 23:02:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (461 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:02:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180773/SRX3180773.20_summits.bed INFO @ Wed, 08 Dec 2021 23:03:01: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (198 records, 4 fields): 2 millis CompletedMACS2peakCalling