Job ID = 16435585 SRX = SRX13110366 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:48:30 prefetch.2.10.7: 1) Downloading 'SRR16918036'... 2022-08-02T01:48:30 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:49:05 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:49:06 prefetch.2.10.7: 'SRR16918036' is valid 2022-08-02T01:49:06 prefetch.2.10.7: 1) 'SRR16918036' was downloaded successfully 2022-08-02T01:49:06 prefetch.2.10.7: 'SRR16918036' has 0 unresolved dependencies Read 20011055 spots for SRR16918036/SRR16918036.sra Written 20011055 spots for SRR16918036/SRR16918036.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436140 ("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: 00:03:27 20011055 reads; of these: 20011055 (100.00%) were unpaired; of these: 14789565 (73.91%) aligned 0 times 4379665 (21.89%) aligned exactly 1 time 841825 (4.21%) aligned >1 times 26.09% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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_rmdupse_core] 579062 / 5221490 = 0.1109 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 10:55:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.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 10:55:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:55:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:55:32: 1000000 INFO @ Tue, 02 Aug 2022 10:55:39: 2000000 INFO @ Tue, 02 Aug 2022 10:55:46: 3000000 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 10:55:53: 4000000 INFO @ Tue, 02 Aug 2022 10:55:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.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 10:55:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:55:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:55:58: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:55:58: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:55:58: #1 total tags in treatment: 4642428 INFO @ Tue, 02 Aug 2022 10:55:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:55:58: #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 10:55:58: #1 tags after filtering in treatment: 4642428 INFO @ Tue, 02 Aug 2022 10:55:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:55:58: #1 finished! INFO @ Tue, 02 Aug 2022 10:55:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:55:58: #2 number of paired peaks: 350 WARNING @ Tue, 02 Aug 2022 10:55:58: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 02 Aug 2022 10:55:59: start model_add_line... INFO @ Tue, 02 Aug 2022 10:55:59: start X-correlation... INFO @ Tue, 02 Aug 2022 10:55:59: end of X-cor INFO @ Tue, 02 Aug 2022 10:55:59: #2 finished! INFO @ Tue, 02 Aug 2022 10:55:59: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:55:59: #2 alternative fragment length(s) may be 74,528 bps INFO @ Tue, 02 Aug 2022 10:55:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.05_model.r WARNING @ Tue, 02 Aug 2022 10:55:59: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:55:59: #2 You may need to consider one of the other alternative d(s): 74,528 WARNING @ Tue, 02 Aug 2022 10:55:59: #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 10:55:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:56:02: 1000000 INFO @ Tue, 02 Aug 2022 10:56:08: 2000000 INFO @ Tue, 02 Aug 2022 10:56:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:56:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:56:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:56:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.05_summits.bed INFO @ Tue, 02 Aug 2022 10:56:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (624 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:56:15: 3000000 INFO @ Tue, 02 Aug 2022 10:56:21: 4000000 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 10:56:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.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 10:56:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:56:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:56:25: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:56:25: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:56:25: #1 total tags in treatment: 4642428 INFO @ Tue, 02 Aug 2022 10:56:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:56:25: #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 10:56:25: #1 tags after filtering in treatment: 4642428 INFO @ Tue, 02 Aug 2022 10:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:56:25: #1 finished! INFO @ Tue, 02 Aug 2022 10:56:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:56:26: #2 number of paired peaks: 350 WARNING @ Tue, 02 Aug 2022 10:56:26: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 02 Aug 2022 10:56:26: start model_add_line... INFO @ Tue, 02 Aug 2022 10:56:26: start X-correlation... INFO @ Tue, 02 Aug 2022 10:56:26: end of X-cor INFO @ Tue, 02 Aug 2022 10:56:26: #2 finished! INFO @ Tue, 02 Aug 2022 10:56:26: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:56:26: #2 alternative fragment length(s) may be 74,528 bps INFO @ Tue, 02 Aug 2022 10:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.10_model.r WARNING @ Tue, 02 Aug 2022 10:56:26: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:56:26: #2 You may need to consider one of the other alternative d(s): 74,528 WARNING @ Tue, 02 Aug 2022 10:56:26: #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 10:56:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:56:31: 1000000 INFO @ Tue, 02 Aug 2022 10:56:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:56:38: 2000000 INFO @ Tue, 02 Aug 2022 10:56:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:56:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:56:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.10_summits.bed INFO @ Tue, 02 Aug 2022 10:56:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:56:44: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:56:51: 4000000 INFO @ Tue, 02 Aug 2022 10:56:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:56:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:56:55: #1 total tags in treatment: 4642428 INFO @ Tue, 02 Aug 2022 10:56:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:56:55: #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 10:56:55: #1 tags after filtering in treatment: 4642428 INFO @ Tue, 02 Aug 2022 10:56:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:56:55: #1 finished! INFO @ Tue, 02 Aug 2022 10:56:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:56:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:56:56: #2 number of paired peaks: 350 WARNING @ Tue, 02 Aug 2022 10:56:56: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 02 Aug 2022 10:56:56: start model_add_line... INFO @ Tue, 02 Aug 2022 10:56:56: start X-correlation... INFO @ Tue, 02 Aug 2022 10:56:56: end of X-cor INFO @ Tue, 02 Aug 2022 10:56:56: #2 finished! INFO @ Tue, 02 Aug 2022 10:56:56: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:56:56: #2 alternative fragment length(s) may be 74,528 bps INFO @ Tue, 02 Aug 2022 10:56:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.20_model.r WARNING @ Tue, 02 Aug 2022 10:56:56: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:56:56: #2 You may need to consider one of the other alternative d(s): 74,528 WARNING @ Tue, 02 Aug 2022 10:56:56: #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 10:56:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:56:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:57:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:57:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:57:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:57:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110366/SRX13110366.20_summits.bed INFO @ Tue, 02 Aug 2022 10:57:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (154 records, 4 fields): 2 millis CompletedMACS2peakCalling