Job ID = 16432242 SRX = SRX15407773 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:31:55 prefetch.2.10.7: 1) Downloading 'SRR19348977'... 2022-08-02T00:31:55 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:32:51 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:32:51 prefetch.2.10.7: 1) 'SRR19348977' was downloaded successfully 2022-08-02T00:32:51 prefetch.2.10.7: 'SRR19348977' has 0 unresolved dependencies Read 29489415 spots for SRR19348977/SRR19348977.sra Written 29489415 spots for SRR19348977/SRR19348977.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434049 ("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: 00:08:19 29489415 reads; of these: 29489415 (100.00%) were unpaired; of these: 2643246 (8.96%) aligned 0 times 22724351 (77.06%) aligned exactly 1 time 4121818 (13.98%) aligned >1 times 91.04% overall alignment rate Time searching: 00:08:19 Overall time: 00:08:19 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 12 files... [bam_rmdupse_core] 5771424 / 26846169 = 0.2150 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 09:49:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.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 09:49:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:49:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:49:06: 1000000 INFO @ Tue, 02 Aug 2022 09:49:12: 2000000 INFO @ Tue, 02 Aug 2022 09:49:18: 3000000 INFO @ Tue, 02 Aug 2022 09:49:24: 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 09:49:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.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 09:49:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:49:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:49:31: 5000000 INFO @ Tue, 02 Aug 2022 09:49:37: 1000000 INFO @ Tue, 02 Aug 2022 09:49:38: 6000000 INFO @ Tue, 02 Aug 2022 09:49:45: 7000000 INFO @ Tue, 02 Aug 2022 09:49:45: 2000000 INFO @ Tue, 02 Aug 2022 09:49:52: 8000000 INFO @ Tue, 02 Aug 2022 09:49:54: 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 09:49:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.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 09:49:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:49:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:50:00: 9000000 INFO @ Tue, 02 Aug 2022 09:50:02: 4000000 INFO @ Tue, 02 Aug 2022 09:50:07: 10000000 INFO @ Tue, 02 Aug 2022 09:50:08: 1000000 INFO @ Tue, 02 Aug 2022 09:50:10: 5000000 INFO @ Tue, 02 Aug 2022 09:50:15: 11000000 INFO @ Tue, 02 Aug 2022 09:50:16: 2000000 INFO @ Tue, 02 Aug 2022 09:50:18: 6000000 INFO @ Tue, 02 Aug 2022 09:50:22: 12000000 INFO @ Tue, 02 Aug 2022 09:50:24: 3000000 INFO @ Tue, 02 Aug 2022 09:50:26: 7000000 INFO @ Tue, 02 Aug 2022 09:50:30: 13000000 INFO @ Tue, 02 Aug 2022 09:50:32: 4000000 INFO @ Tue, 02 Aug 2022 09:50:34: 8000000 INFO @ Tue, 02 Aug 2022 09:50:38: 14000000 INFO @ Tue, 02 Aug 2022 09:50:41: 5000000 INFO @ Tue, 02 Aug 2022 09:50:42: 9000000 INFO @ Tue, 02 Aug 2022 09:50:45: 15000000 INFO @ Tue, 02 Aug 2022 09:50:49: 6000000 INFO @ Tue, 02 Aug 2022 09:50:50: 10000000 INFO @ Tue, 02 Aug 2022 09:50:53: 16000000 INFO @ Tue, 02 Aug 2022 09:50:57: 7000000 INFO @ Tue, 02 Aug 2022 09:50:59: 11000000 INFO @ Tue, 02 Aug 2022 09:51:01: 17000000 INFO @ Tue, 02 Aug 2022 09:51:05: 8000000 INFO @ Tue, 02 Aug 2022 09:51:07: 12000000 INFO @ Tue, 02 Aug 2022 09:51:08: 18000000 INFO @ Tue, 02 Aug 2022 09:51:13: 9000000 INFO @ Tue, 02 Aug 2022 09:51:16: 13000000 INFO @ Tue, 02 Aug 2022 09:51:16: 19000000 INFO @ Tue, 02 Aug 2022 09:51:22: 10000000 INFO @ Tue, 02 Aug 2022 09:51:24: 20000000 INFO @ Tue, 02 Aug 2022 09:51:24: 14000000 INFO @ Tue, 02 Aug 2022 09:51:30: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:51:31: 21000000 INFO @ Tue, 02 Aug 2022 09:51:32: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:51:32: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:51:32: #1 total tags in treatment: 21074745 INFO @ Tue, 02 Aug 2022 09:51:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:51:32: #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 09:51:32: #1 tags after filtering in treatment: 21074745 INFO @ Tue, 02 Aug 2022 09:51:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:51:32: #1 finished! INFO @ Tue, 02 Aug 2022 09:51:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:51:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:51:32: 15000000 INFO @ Tue, 02 Aug 2022 09:51:33: #2 number of paired peaks: 154 WARNING @ Tue, 02 Aug 2022 09:51:33: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Tue, 02 Aug 2022 09:51:33: start model_add_line... INFO @ Tue, 02 Aug 2022 09:51:34: start X-correlation... INFO @ Tue, 02 Aug 2022 09:51:34: end of X-cor INFO @ Tue, 02 Aug 2022 09:51:34: #2 finished! INFO @ Tue, 02 Aug 2022 09:51:34: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 09:51:34: #2 alternative fragment length(s) may be 1,36,66,598 bps INFO @ Tue, 02 Aug 2022 09:51:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.05_model.r WARNING @ Tue, 02 Aug 2022 09:51:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:51:34: #2 You may need to consider one of the other alternative d(s): 1,36,66,598 WARNING @ Tue, 02 Aug 2022 09:51:34: #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 09:51:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:51:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:51:38: 12000000 INFO @ Tue, 02 Aug 2022 09:51:40: 16000000 INFO @ Tue, 02 Aug 2022 09:51:47: 13000000 INFO @ Tue, 02 Aug 2022 09:51:48: 17000000 INFO @ Tue, 02 Aug 2022 09:51:54: 14000000 INFO @ Tue, 02 Aug 2022 09:51:56: 18000000 INFO @ Tue, 02 Aug 2022 09:52:02: 15000000 INFO @ Tue, 02 Aug 2022 09:52:04: 19000000 INFO @ Tue, 02 Aug 2022 09:52:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:52:10: 16000000 INFO @ Tue, 02 Aug 2022 09:52:11: 20000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:52:17: 17000000 INFO @ Tue, 02 Aug 2022 09:52:19: 21000000 INFO @ Tue, 02 Aug 2022 09:52:20: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:52:20: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:52:20: #1 total tags in treatment: 21074745 INFO @ Tue, 02 Aug 2022 09:52:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:52:20: #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 09:52:20: #1 tags after filtering in treatment: 21074745 INFO @ Tue, 02 Aug 2022 09:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:52:20: #1 finished! INFO @ Tue, 02 Aug 2022 09:52:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:52:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:52:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:52:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.05_summits.bed INFO @ Tue, 02 Aug 2022 09:52:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:52:21: #2 number of paired peaks: 154 WARNING @ Tue, 02 Aug 2022 09:52:21: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Tue, 02 Aug 2022 09:52:21: start model_add_line... INFO @ Tue, 02 Aug 2022 09:52:21: start X-correlation... INFO @ Tue, 02 Aug 2022 09:52:21: end of X-cor INFO @ Tue, 02 Aug 2022 09:52:21: #2 finished! INFO @ Tue, 02 Aug 2022 09:52:21: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 09:52:21: #2 alternative fragment length(s) may be 1,36,66,598 bps INFO @ Tue, 02 Aug 2022 09:52:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.10_model.r WARNING @ Tue, 02 Aug 2022 09:52:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:52:21: #2 You may need to consider one of the other alternative d(s): 1,36,66,598 WARNING @ Tue, 02 Aug 2022 09:52:21: #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 09:52:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:52:24: 18000000 INFO @ Tue, 02 Aug 2022 09:52:31: 19000000 INFO @ Tue, 02 Aug 2022 09:52:38: 20000000 INFO @ Tue, 02 Aug 2022 09:52:44: 21000000 INFO @ Tue, 02 Aug 2022 09:52:45: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:52:45: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:52:45: #1 total tags in treatment: 21074745 INFO @ Tue, 02 Aug 2022 09:52:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:52:45: #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 09:52:45: #1 tags after filtering in treatment: 21074745 INFO @ Tue, 02 Aug 2022 09:52:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:52:45: #1 finished! INFO @ Tue, 02 Aug 2022 09:52:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:52:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:52:46: #2 number of paired peaks: 154 WARNING @ Tue, 02 Aug 2022 09:52:46: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Tue, 02 Aug 2022 09:52:46: start model_add_line... INFO @ Tue, 02 Aug 2022 09:52:46: start X-correlation... INFO @ Tue, 02 Aug 2022 09:52:46: end of X-cor INFO @ Tue, 02 Aug 2022 09:52:46: #2 finished! INFO @ Tue, 02 Aug 2022 09:52:46: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 09:52:46: #2 alternative fragment length(s) may be 1,36,66,598 bps INFO @ Tue, 02 Aug 2022 09:52:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.20_model.r WARNING @ Tue, 02 Aug 2022 09:52:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:52:46: #2 You may need to consider one of the other alternative d(s): 1,36,66,598 WARNING @ Tue, 02 Aug 2022 09:52:46: #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 09:52:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:52:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:52:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:53:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.10_summits.bed INFO @ Tue, 02 Aug 2022 09:53:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:53:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:53:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407773/SRX15407773.20_summits.bed INFO @ Tue, 02 Aug 2022 09:53:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling