Job ID = 16435597 SRX = SRX13110379 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:52:30 prefetch.2.10.7: 1) Downloading 'SRR16918049'... 2022-08-02T01:52:30 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:52:58 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:52:59 prefetch.2.10.7: 'SRR16918049' is valid 2022-08-02T01:52:59 prefetch.2.10.7: 1) 'SRR16918049' was downloaded successfully 2022-08-02T01:52:59 prefetch.2.10.7: 'SRR16918049' has 0 unresolved dependencies Read 15606384 spots for SRR16918049/SRR16918049.sra Written 15606384 spots for SRR16918049/SRR16918049.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436165 ("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: 00:04:46 15606384 reads; of these: 15606384 (100.00%) were unpaired; of these: 370736 (2.38%) aligned 0 times 12870003 (82.47%) aligned exactly 1 time 2365645 (15.16%) aligned >1 times 97.62% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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] 1544457 / 15235648 = 0.1014 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 11:02:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.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 11:02:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:02:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:02:30: 1000000 INFO @ Tue, 02 Aug 2022 11:02:37: 2000000 INFO @ Tue, 02 Aug 2022 11:02:44: 3000000 INFO @ Tue, 02 Aug 2022 11:02:51: 4000000 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 11:02:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.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 11:02:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:02:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:02:58: 5000000 INFO @ Tue, 02 Aug 2022 11:03:00: 1000000 INFO @ Tue, 02 Aug 2022 11:03:05: 6000000 INFO @ Tue, 02 Aug 2022 11:03:07: 2000000 INFO @ Tue, 02 Aug 2022 11:03:13: 7000000 INFO @ Tue, 02 Aug 2022 11:03:14: 3000000 INFO @ Tue, 02 Aug 2022 11:03:20: 8000000 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 11:03:22: 4000000 INFO @ Tue, 02 Aug 2022 11:03:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.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 11:03:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:03:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:03:26: 9000000 INFO @ Tue, 02 Aug 2022 11:03:29: 5000000 INFO @ Tue, 02 Aug 2022 11:03:30: 1000000 INFO @ Tue, 02 Aug 2022 11:03:33: 10000000 INFO @ Tue, 02 Aug 2022 11:03:37: 6000000 INFO @ Tue, 02 Aug 2022 11:03:38: 2000000 INFO @ Tue, 02 Aug 2022 11:03:40: 11000000 INFO @ Tue, 02 Aug 2022 11:03:44: 7000000 INFO @ Tue, 02 Aug 2022 11:03:46: 3000000 INFO @ Tue, 02 Aug 2022 11:03:47: 12000000 INFO @ Tue, 02 Aug 2022 11:03:52: 8000000 INFO @ Tue, 02 Aug 2022 11:03:54: 4000000 INFO @ Tue, 02 Aug 2022 11:03:54: 13000000 INFO @ Tue, 02 Aug 2022 11:03:59: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:03:59: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:03:59: #1 total tags in treatment: 13691191 INFO @ Tue, 02 Aug 2022 11:03:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:03:59: #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 11:03:59: #1 tags after filtering in treatment: 13691191 INFO @ Tue, 02 Aug 2022 11:03:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:03:59: #1 finished! INFO @ Tue, 02 Aug 2022 11:03:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:03:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:04:00: 9000000 INFO @ Tue, 02 Aug 2022 11:04:00: #2 number of paired peaks: 232 WARNING @ Tue, 02 Aug 2022 11:04:00: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 02 Aug 2022 11:04:00: start model_add_line... INFO @ Tue, 02 Aug 2022 11:04:00: start X-correlation... INFO @ Tue, 02 Aug 2022 11:04:00: end of X-cor INFO @ Tue, 02 Aug 2022 11:04:00: #2 finished! INFO @ Tue, 02 Aug 2022 11:04:00: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 11:04:00: #2 alternative fragment length(s) may be 4,74,547 bps INFO @ Tue, 02 Aug 2022 11:04:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.05_model.r WARNING @ Tue, 02 Aug 2022 11:04:00: #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 11:04:00: #2 You may need to consider one of the other alternative d(s): 4,74,547 WARNING @ Tue, 02 Aug 2022 11:04:00: #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 11:04:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:04:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:04:01: 5000000 INFO @ Tue, 02 Aug 2022 11:04:07: 10000000 INFO @ Tue, 02 Aug 2022 11:04:09: 6000000 INFO @ Tue, 02 Aug 2022 11:04:15: 11000000 INFO @ Tue, 02 Aug 2022 11:04:16: 7000000 INFO @ Tue, 02 Aug 2022 11:04:23: 12000000 INFO @ Tue, 02 Aug 2022 11:04:23: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:04:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:04:30: 9000000 INFO @ Tue, 02 Aug 2022 11:04:30: 13000000 INFO @ Tue, 02 Aug 2022 11:04:35: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:04:35: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:04:35: #1 total tags in treatment: 13691191 INFO @ Tue, 02 Aug 2022 11:04:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:04:35: #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 11:04:36: #1 tags after filtering in treatment: 13691191 INFO @ Tue, 02 Aug 2022 11:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:04:36: #1 finished! INFO @ Tue, 02 Aug 2022 11:04:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:04:36: 10000000 INFO @ Tue, 02 Aug 2022 11:04:37: #2 number of paired peaks: 232 WARNING @ Tue, 02 Aug 2022 11:04:37: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 02 Aug 2022 11:04:37: start model_add_line... INFO @ Tue, 02 Aug 2022 11:04:37: start X-correlation... INFO @ Tue, 02 Aug 2022 11:04:37: end of X-cor INFO @ Tue, 02 Aug 2022 11:04:37: #2 finished! INFO @ Tue, 02 Aug 2022 11:04:37: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 11:04:37: #2 alternative fragment length(s) may be 4,74,547 bps INFO @ Tue, 02 Aug 2022 11:04:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.10_model.r WARNING @ Tue, 02 Aug 2022 11:04:37: #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 11:04:37: #2 You may need to consider one of the other alternative d(s): 4,74,547 WARNING @ Tue, 02 Aug 2022 11:04:37: #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 11:04:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:04:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:04:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:04:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:04:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.05_summits.bed INFO @ Tue, 02 Aug 2022 11:04:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (633 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:04:42: 11000000 INFO @ Tue, 02 Aug 2022 11:04:48: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:04:53: 13000000 INFO @ Tue, 02 Aug 2022 11:04:57: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:04:57: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:04:57: #1 total tags in treatment: 13691191 INFO @ Tue, 02 Aug 2022 11:04:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:04:57: #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 11:04:57: #1 tags after filtering in treatment: 13691191 INFO @ Tue, 02 Aug 2022 11:04:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:04:57: #1 finished! INFO @ Tue, 02 Aug 2022 11:04:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:04:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:04:58: #2 number of paired peaks: 232 WARNING @ Tue, 02 Aug 2022 11:04:58: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 02 Aug 2022 11:04:58: start model_add_line... INFO @ Tue, 02 Aug 2022 11:04:58: start X-correlation... INFO @ Tue, 02 Aug 2022 11:04:58: end of X-cor INFO @ Tue, 02 Aug 2022 11:04:58: #2 finished! INFO @ Tue, 02 Aug 2022 11:04:58: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 11:04:58: #2 alternative fragment length(s) may be 4,74,547 bps INFO @ Tue, 02 Aug 2022 11:04:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.20_model.r WARNING @ Tue, 02 Aug 2022 11:04:59: #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 11:04:59: #2 You may need to consider one of the other alternative d(s): 4,74,547 WARNING @ Tue, 02 Aug 2022 11:04:59: #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 11:04:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:04:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:05:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:05:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:05:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:05:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.10_summits.bed INFO @ Tue, 02 Aug 2022 11:05:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (406 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:05:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:05:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:05:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:05:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110379/SRX13110379.20_summits.bed INFO @ Tue, 02 Aug 2022 11:05:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 36 millis CompletedMACS2peakCalling