Job ID = 16432422 SRX = SRX15407786 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:32:11 prefetch.2.10.7: 1) Downloading 'SRR19348964'... 2022-08-02T00:32:11 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:32:39 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:32:40 prefetch.2.10.7: 'SRR19348964' is valid 2022-08-02T00:32:40 prefetch.2.10.7: 1) 'SRR19348964' was downloaded successfully 2022-08-02T00:32:40 prefetch.2.10.7: 'SRR19348964' has 0 unresolved dependencies Read 14012679 spots for SRR19348964/SRR19348964.sra Written 14012679 spots for SRR19348964/SRR19348964.sra fastq に変換しました。 bowtie でマッピング中... Your job 16433464 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:04:21 14012679 reads; of these: 14012679 (100.00%) were unpaired; of these: 1305272 (9.31%) aligned 0 times 10845974 (77.40%) aligned exactly 1 time 1861433 (13.28%) aligned >1 times 90.69% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 1139992 / 12707407 = 0.0897 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 09:42:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.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 09:42:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:42:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:42:13: 1000000 INFO @ Tue, 02 Aug 2022 09:42:19: 2000000 INFO @ Tue, 02 Aug 2022 09:42:24: 3000000 INFO @ Tue, 02 Aug 2022 09:42:30: 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 09:42:36: 5000000 INFO @ Tue, 02 Aug 2022 09:42:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.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 09:42:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:42:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:42:41: 6000000 INFO @ Tue, 02 Aug 2022 09:42:42: 1000000 INFO @ Tue, 02 Aug 2022 09:42:46: 7000000 INFO @ Tue, 02 Aug 2022 09:42:47: 2000000 INFO @ Tue, 02 Aug 2022 09:42:52: 8000000 INFO @ Tue, 02 Aug 2022 09:42:53: 3000000 INFO @ Tue, 02 Aug 2022 09:42:57: 9000000 INFO @ Tue, 02 Aug 2022 09:42:58: 4000000 INFO @ Tue, 02 Aug 2022 09:43:03: 10000000 INFO @ Tue, 02 Aug 2022 09:43:04: 5000000 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 09:43:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.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 09:43:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:43:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:43:09: 11000000 INFO @ Tue, 02 Aug 2022 09:43:09: 6000000 INFO @ Tue, 02 Aug 2022 09:43:13: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:43:13: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:43:13: #1 total tags in treatment: 11567415 INFO @ Tue, 02 Aug 2022 09:43:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:43:13: #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 09:43:13: #1 tags after filtering in treatment: 11567415 INFO @ Tue, 02 Aug 2022 09:43:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:43:13: #1 finished! INFO @ Tue, 02 Aug 2022 09:43:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:43:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:43:13: 1000000 INFO @ Tue, 02 Aug 2022 09:43:14: #2 number of paired peaks: 247 WARNING @ Tue, 02 Aug 2022 09:43:14: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 02 Aug 2022 09:43:14: start model_add_line... INFO @ Tue, 02 Aug 2022 09:43:14: start X-correlation... INFO @ Tue, 02 Aug 2022 09:43:14: end of X-cor INFO @ Tue, 02 Aug 2022 09:43:14: #2 finished! INFO @ Tue, 02 Aug 2022 09:43:14: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 09:43:14: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 09:43:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.05_model.r WARNING @ Tue, 02 Aug 2022 09:43:14: #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 09:43:14: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 09:43:14: #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 09:43:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:43:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:43:14: 7000000 INFO @ Tue, 02 Aug 2022 09:43:19: 2000000 INFO @ Tue, 02 Aug 2022 09:43:20: 8000000 INFO @ Tue, 02 Aug 2022 09:43:25: 3000000 INFO @ Tue, 02 Aug 2022 09:43:26: 9000000 INFO @ Tue, 02 Aug 2022 09:43:30: 4000000 INFO @ Tue, 02 Aug 2022 09:43:32: 10000000 INFO @ Tue, 02 Aug 2022 09:43:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:43:36: 5000000 INFO @ Tue, 02 Aug 2022 09:43:38: 11000000 INFO @ Tue, 02 Aug 2022 09:43:41: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:43:41: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:43:41: #1 total tags in treatment: 11567415 INFO @ Tue, 02 Aug 2022 09:43:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:43:41: #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 09:43:41: #1 tags after filtering in treatment: 11567415 INFO @ Tue, 02 Aug 2022 09:43:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:43:41: #1 finished! INFO @ Tue, 02 Aug 2022 09:43:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:43:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:43:42: 6000000 INFO @ Tue, 02 Aug 2022 09:43:42: #2 number of paired peaks: 247 WARNING @ Tue, 02 Aug 2022 09:43:42: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 02 Aug 2022 09:43:42: start model_add_line... INFO @ Tue, 02 Aug 2022 09:43:42: start X-correlation... INFO @ Tue, 02 Aug 2022 09:43:42: end of X-cor INFO @ Tue, 02 Aug 2022 09:43:42: #2 finished! INFO @ Tue, 02 Aug 2022 09:43:42: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 09:43:42: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 09:43:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.10_model.r WARNING @ Tue, 02 Aug 2022 09:43:42: #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 09:43:42: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 09:43:42: #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 09:43:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:43:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:43:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:43:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:43:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.05_summits.bed INFO @ Tue, 02 Aug 2022 09:43:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (683 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:43:47: 7000000 INFO @ Tue, 02 Aug 2022 09:43:53: 8000000 INFO @ Tue, 02 Aug 2022 09:43:58: 9000000 INFO @ Tue, 02 Aug 2022 09:44:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:44:04: 10000000 INFO @ Tue, 02 Aug 2022 09:44:09: 11000000 INFO @ Tue, 02 Aug 2022 09:44:12: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:44:12: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:44:12: #1 total tags in treatment: 11567415 INFO @ Tue, 02 Aug 2022 09:44:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:44:12: #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 09:44:12: #1 tags after filtering in treatment: 11567415 INFO @ Tue, 02 Aug 2022 09:44:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:44:12: #1 finished! INFO @ Tue, 02 Aug 2022 09:44:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:44:13: #2 number of paired peaks: 247 WARNING @ Tue, 02 Aug 2022 09:44:13: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 02 Aug 2022 09:44:13: start model_add_line... INFO @ Tue, 02 Aug 2022 09:44:13: start X-correlation... INFO @ Tue, 02 Aug 2022 09:44:13: end of X-cor INFO @ Tue, 02 Aug 2022 09:44:13: #2 finished! INFO @ Tue, 02 Aug 2022 09:44:13: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 09:44:13: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 09:44:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.20_model.r WARNING @ Tue, 02 Aug 2022 09:44:13: #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 09:44:13: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 09:44:13: #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 09:44:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:44:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:44:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:44:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:44:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.10_summits.bed INFO @ Tue, 02 Aug 2022 09:44:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (366 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:44:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:44:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:44:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:44:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407786/SRX15407786.20_summits.bed INFO @ Tue, 02 Aug 2022 09:44:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (207 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。