Job ID = 16435581 SRX = SRX13110360 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:47:31 prefetch.2.10.7: 1) Downloading 'SRR16918030'... 2022-08-02T01:47:31 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:48:10 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:48:11 prefetch.2.10.7: 'SRR16918030' is valid 2022-08-02T01:48:11 prefetch.2.10.7: 1) 'SRR16918030' was downloaded successfully 2022-08-02T01:48:11 prefetch.2.10.7: 'SRR16918030' has 0 unresolved dependencies Read 19177135 spots for SRR16918030/SRR16918030.sra Written 19177135 spots for SRR16918030/SRR16918030.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436145 ("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: 00:05:23 19177135 reads; of these: 19177135 (100.00%) were unpaired; of these: 6735565 (35.12%) aligned 0 times 10649231 (55.53%) aligned exactly 1 time 1792339 (9.35%) aligned >1 times 64.88% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 1163692 / 12441570 = 0.0935 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 10:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.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 10:58:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:58:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:58:10: 1000000 INFO @ Tue, 02 Aug 2022 10:58:17: 2000000 INFO @ Tue, 02 Aug 2022 10:58:23: 3000000 INFO @ Tue, 02 Aug 2022 10:58:29: 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 10:58:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.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 10:58:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:58:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:58:35: 5000000 INFO @ Tue, 02 Aug 2022 10:58:41: 1000000 INFO @ Tue, 02 Aug 2022 10:58:42: 6000000 INFO @ Tue, 02 Aug 2022 10:58:49: 2000000 INFO @ Tue, 02 Aug 2022 10:58:49: 7000000 INFO @ Tue, 02 Aug 2022 10:58:56: 8000000 INFO @ Tue, 02 Aug 2022 10:58:56: 3000000 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 10:59:02: 9000000 INFO @ Tue, 02 Aug 2022 10:59:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.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 10:59:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:59:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:59:04: 4000000 INFO @ Tue, 02 Aug 2022 10:59:10: 10000000 INFO @ Tue, 02 Aug 2022 10:59:11: 1000000 INFO @ Tue, 02 Aug 2022 10:59:12: 5000000 INFO @ Tue, 02 Aug 2022 10:59:16: 11000000 INFO @ Tue, 02 Aug 2022 10:59:18: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:59:18: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:59:18: #1 total tags in treatment: 11277878 INFO @ Tue, 02 Aug 2022 10:59:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:59:18: #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 10:59:18: 2000000 INFO @ Tue, 02 Aug 2022 10:59:19: #1 tags after filtering in treatment: 11277878 INFO @ Tue, 02 Aug 2022 10:59:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:59:19: #1 finished! INFO @ Tue, 02 Aug 2022 10:59:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:59:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:59:19: #2 number of paired peaks: 238 WARNING @ Tue, 02 Aug 2022 10:59:19: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 02 Aug 2022 10:59:19: start model_add_line... INFO @ Tue, 02 Aug 2022 10:59:19: start X-correlation... INFO @ Tue, 02 Aug 2022 10:59:19: end of X-cor INFO @ Tue, 02 Aug 2022 10:59:19: #2 finished! INFO @ Tue, 02 Aug 2022 10:59:19: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:59:19: #2 alternative fragment length(s) may be 4,71,541 bps INFO @ Tue, 02 Aug 2022 10:59:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.05_model.r WARNING @ Tue, 02 Aug 2022 10:59:19: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:59:19: #2 You may need to consider one of the other alternative d(s): 4,71,541 WARNING @ Tue, 02 Aug 2022 10:59:19: #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 10:59:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:59:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:59:19: 6000000 INFO @ Tue, 02 Aug 2022 10:59:26: 3000000 INFO @ Tue, 02 Aug 2022 10:59:27: 7000000 INFO @ Tue, 02 Aug 2022 10:59:33: 4000000 INFO @ Tue, 02 Aug 2022 10:59:35: 8000000 INFO @ Tue, 02 Aug 2022 10:59:41: 5000000 INFO @ Tue, 02 Aug 2022 10:59:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:59:43: 9000000 INFO @ Tue, 02 Aug 2022 10:59:48: 6000000 INFO @ Tue, 02 Aug 2022 10:59:50: 10000000 INFO @ Tue, 02 Aug 2022 10:59:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:59:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:59:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.05_summits.bed INFO @ Tue, 02 Aug 2022 10:59:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (778 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:59:54: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:59:58: 11000000 INFO @ Tue, 02 Aug 2022 11:00:00: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:00:00: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:00:00: #1 total tags in treatment: 11277878 INFO @ Tue, 02 Aug 2022 11:00:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:00:00: #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 11:00:00: #1 tags after filtering in treatment: 11277878 INFO @ Tue, 02 Aug 2022 11:00:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:00:00: #1 finished! INFO @ Tue, 02 Aug 2022 11:00:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:00:01: 8000000 INFO @ Tue, 02 Aug 2022 11:00:01: #2 number of paired peaks: 238 WARNING @ Tue, 02 Aug 2022 11:00:01: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 02 Aug 2022 11:00:01: start model_add_line... INFO @ Tue, 02 Aug 2022 11:00:01: start X-correlation... INFO @ Tue, 02 Aug 2022 11:00:01: end of X-cor INFO @ Tue, 02 Aug 2022 11:00:01: #2 finished! INFO @ Tue, 02 Aug 2022 11:00:01: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 11:00:01: #2 alternative fragment length(s) may be 4,71,541 bps INFO @ Tue, 02 Aug 2022 11:00:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.10_model.r WARNING @ Tue, 02 Aug 2022 11:00:01: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:00:01: #2 You may need to consider one of the other alternative d(s): 4,71,541 WARNING @ Tue, 02 Aug 2022 11:00:01: #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 11:00:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:00:07: 9000000 INFO @ Tue, 02 Aug 2022 11:00:13: 10000000 INFO @ Tue, 02 Aug 2022 11:00:20: 11000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:00:21: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:00:21: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:00:21: #1 total tags in treatment: 11277878 INFO @ Tue, 02 Aug 2022 11:00:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:00:21: #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 11:00:22: #1 tags after filtering in treatment: 11277878 INFO @ Tue, 02 Aug 2022 11:00:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:00:22: #1 finished! INFO @ Tue, 02 Aug 2022 11:00:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:00:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:00:22: #2 number of paired peaks: 238 WARNING @ Tue, 02 Aug 2022 11:00:22: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 02 Aug 2022 11:00:22: start model_add_line... INFO @ Tue, 02 Aug 2022 11:00:22: start X-correlation... INFO @ Tue, 02 Aug 2022 11:00:22: end of X-cor INFO @ Tue, 02 Aug 2022 11:00:22: #2 finished! INFO @ Tue, 02 Aug 2022 11:00:22: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 11:00:22: #2 alternative fragment length(s) may be 4,71,541 bps INFO @ Tue, 02 Aug 2022 11:00:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.20_model.r WARNING @ Tue, 02 Aug 2022 11:00:22: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:00:22: #2 You may need to consider one of the other alternative d(s): 4,71,541 WARNING @ Tue, 02 Aug 2022 11:00:22: #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 11:00:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:00:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.10_summits.bed INFO @ Tue, 02 Aug 2022 11:00:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (368 records, 4 fields): 119 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:00:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:00:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:00:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:00:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110360/SRX13110360.20_summits.bed INFO @ Tue, 02 Aug 2022 11:00:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 16 millis CompletedMACS2peakCalling