Job ID = 16436117 SRX = SRX13110392 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:55:03 prefetch.2.10.7: 1) Downloading 'SRR16918062'... 2022-08-02T01:55:03 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:55:32 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:55:32 prefetch.2.10.7: 'SRR16918062' is valid 2022-08-02T01:55:32 prefetch.2.10.7: 1) 'SRR16918062' was downloaded successfully 2022-08-02T01:55:32 prefetch.2.10.7: 'SRR16918062' has 0 unresolved dependencies Read 16432844 spots for SRR16918062/SRR16918062.sra Written 16432844 spots for SRR16918062/SRR16918062.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436198 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:21 16432844 reads; of these: 16432844 (100.00%) were unpaired; of these: 927418 (5.64%) aligned 0 times 12939125 (78.74%) aligned exactly 1 time 2566301 (15.62%) aligned >1 times 94.36% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 1492036 / 15505426 = 0.0962 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 11:05:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.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 11:05:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:05:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:05:56: 1000000 INFO @ Tue, 02 Aug 2022 11:06:04: 2000000 INFO @ Tue, 02 Aug 2022 11:06:11: 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 11:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.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 11:06:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:06:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:06:19: 4000000 INFO @ Tue, 02 Aug 2022 11:06:27: 1000000 INFO @ Tue, 02 Aug 2022 11:06:27: 5000000 INFO @ Tue, 02 Aug 2022 11:06:36: 6000000 INFO @ Tue, 02 Aug 2022 11:06:36: 2000000 INFO @ Tue, 02 Aug 2022 11:06:44: 7000000 INFO @ Tue, 02 Aug 2022 11:06:45: 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 11:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.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 11:06:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:06:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:06:53: 8000000 INFO @ Tue, 02 Aug 2022 11:06:53: 4000000 INFO @ Tue, 02 Aug 2022 11:06:58: 1000000 INFO @ Tue, 02 Aug 2022 11:07:01: 9000000 INFO @ Tue, 02 Aug 2022 11:07:02: 5000000 INFO @ Tue, 02 Aug 2022 11:07:07: 2000000 INFO @ Tue, 02 Aug 2022 11:07:10: 6000000 INFO @ Tue, 02 Aug 2022 11:07:10: 10000000 INFO @ Tue, 02 Aug 2022 11:07:15: 3000000 INFO @ Tue, 02 Aug 2022 11:07:19: 11000000 INFO @ Tue, 02 Aug 2022 11:07:19: 7000000 INFO @ Tue, 02 Aug 2022 11:07:23: 4000000 INFO @ Tue, 02 Aug 2022 11:07:28: 12000000 INFO @ Tue, 02 Aug 2022 11:07:28: 8000000 INFO @ Tue, 02 Aug 2022 11:07:32: 5000000 INFO @ Tue, 02 Aug 2022 11:07:37: 13000000 INFO @ Tue, 02 Aug 2022 11:07:37: 9000000 INFO @ Tue, 02 Aug 2022 11:07:40: 6000000 INFO @ Tue, 02 Aug 2022 11:07:45: 14000000 INFO @ Tue, 02 Aug 2022 11:07:46: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:07:46: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:07:46: #1 total tags in treatment: 14013390 INFO @ Tue, 02 Aug 2022 11:07:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:07:46: #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 11:07:46: #1 tags after filtering in treatment: 14013390 INFO @ Tue, 02 Aug 2022 11:07:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:07:46: #1 finished! INFO @ Tue, 02 Aug 2022 11:07:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:07:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:07:46: 10000000 INFO @ Tue, 02 Aug 2022 11:07:47: #2 number of paired peaks: 245 WARNING @ Tue, 02 Aug 2022 11:07:47: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Tue, 02 Aug 2022 11:07:47: start model_add_line... INFO @ Tue, 02 Aug 2022 11:07:47: start X-correlation... INFO @ Tue, 02 Aug 2022 11:07:47: end of X-cor INFO @ Tue, 02 Aug 2022 11:07:47: #2 finished! INFO @ Tue, 02 Aug 2022 11:07:47: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 11:07:47: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 11:07:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.05_model.r WARNING @ Tue, 02 Aug 2022 11:07:47: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:07:47: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 11:07:47: #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 11:07:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:07:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:07:48: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:07:55: 11000000 INFO @ Tue, 02 Aug 2022 11:07:56: 8000000 INFO @ Tue, 02 Aug 2022 11:08:03: 9000000 INFO @ Tue, 02 Aug 2022 11:08:04: 12000000 INFO @ Tue, 02 Aug 2022 11:08:11: 10000000 INFO @ Tue, 02 Aug 2022 11:08:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:08:13: 13000000 INFO @ Tue, 02 Aug 2022 11:08:19: 11000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:08:21: 14000000 INFO @ Tue, 02 Aug 2022 11:08:22: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:08:22: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:08:22: #1 total tags in treatment: 14013390 INFO @ Tue, 02 Aug 2022 11:08:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:08:22: #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 11:08:22: #1 tags after filtering in treatment: 14013390 INFO @ Tue, 02 Aug 2022 11:08:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:08:22: #1 finished! INFO @ Tue, 02 Aug 2022 11:08:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:08:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:08:23: #2 number of paired peaks: 245 WARNING @ Tue, 02 Aug 2022 11:08:23: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Tue, 02 Aug 2022 11:08:23: start model_add_line... INFO @ Tue, 02 Aug 2022 11:08:23: start X-correlation... INFO @ Tue, 02 Aug 2022 11:08:23: end of X-cor INFO @ Tue, 02 Aug 2022 11:08:23: #2 finished! INFO @ Tue, 02 Aug 2022 11:08:23: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 11:08:23: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 11:08:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.10_model.r WARNING @ Tue, 02 Aug 2022 11:08:23: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:08:23: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 11:08:23: #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 11:08:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:08:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.05_summits.bed INFO @ Tue, 02 Aug 2022 11:08:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (654 records, 4 fields): 64 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:08:26: 12000000 INFO @ Tue, 02 Aug 2022 11:08:33: 13000000 INFO @ Tue, 02 Aug 2022 11:08:39: 14000000 INFO @ Tue, 02 Aug 2022 11:08:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:08:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:08:39: #1 total tags in treatment: 14013390 INFO @ Tue, 02 Aug 2022 11:08:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:08:39: #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 11:08:39: #1 tags after filtering in treatment: 14013390 INFO @ Tue, 02 Aug 2022 11:08:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:08:39: #1 finished! INFO @ Tue, 02 Aug 2022 11:08:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:08:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:08:40: #2 number of paired peaks: 245 WARNING @ Tue, 02 Aug 2022 11:08:40: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Tue, 02 Aug 2022 11:08:40: start model_add_line... INFO @ Tue, 02 Aug 2022 11:08:40: start X-correlation... INFO @ Tue, 02 Aug 2022 11:08:40: end of X-cor INFO @ Tue, 02 Aug 2022 11:08:40: #2 finished! INFO @ Tue, 02 Aug 2022 11:08:40: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 11:08:40: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 11:08:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.20_model.r WARNING @ Tue, 02 Aug 2022 11:08:40: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:08:40: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 11:08:40: #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 11:08:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:08:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:08:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:09:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:09:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:09:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.10_summits.bed INFO @ Tue, 02 Aug 2022 11:09:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (406 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:09:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:09:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:09:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:09:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110392/SRX13110392.20_summits.bed INFO @ Tue, 02 Aug 2022 11:09:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 42 millis CompletedMACS2peakCalling