Job ID = 16434852 SRX = SRX10435521 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19602543 spots for SRR14060953/SRR14060953.sra Written 19602543 spots for SRR14060953/SRR14060953.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434915 ("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: 00:07:13 19602543 reads; of these: 19602543 (100.00%) were unpaired; of these: 1500637 (7.66%) aligned 0 times 15224493 (77.67%) aligned exactly 1 time 2877413 (14.68%) aligned >1 times 92.34% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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] 1992975 / 18101906 = 0.1101 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 10:16:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.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 10:16:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:16:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:16:59: 1000000 INFO @ Tue, 02 Aug 2022 10:17:07: 2000000 INFO @ Tue, 02 Aug 2022 10:17:14: 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 10:17:21: 4000000 INFO @ Tue, 02 Aug 2022 10:17:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.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 10:17:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:17:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:17:29: 5000000 INFO @ Tue, 02 Aug 2022 10:17:31: 1000000 INFO @ Tue, 02 Aug 2022 10:17:36: 6000000 INFO @ Tue, 02 Aug 2022 10:17:39: 2000000 INFO @ Tue, 02 Aug 2022 10:17:43: 7000000 INFO @ Tue, 02 Aug 2022 10:17:46: 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 10:17:51: 8000000 INFO @ Tue, 02 Aug 2022 10:17:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.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 10:17:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:17:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:17:53: 4000000 INFO @ Tue, 02 Aug 2022 10:17:59: 9000000 INFO @ Tue, 02 Aug 2022 10:18:00: 1000000 INFO @ Tue, 02 Aug 2022 10:18:01: 5000000 INFO @ Tue, 02 Aug 2022 10:18:07: 10000000 INFO @ Tue, 02 Aug 2022 10:18:09: 2000000 INFO @ Tue, 02 Aug 2022 10:18:09: 6000000 INFO @ Tue, 02 Aug 2022 10:18:16: 11000000 INFO @ Tue, 02 Aug 2022 10:18:17: 3000000 INFO @ Tue, 02 Aug 2022 10:18:19: 7000000 INFO @ Tue, 02 Aug 2022 10:18:24: 12000000 INFO @ Tue, 02 Aug 2022 10:18:25: 4000000 INFO @ Tue, 02 Aug 2022 10:18:27: 8000000 INFO @ Tue, 02 Aug 2022 10:18:32: 13000000 INFO @ Tue, 02 Aug 2022 10:18:35: 5000000 INFO @ Tue, 02 Aug 2022 10:18:37: 9000000 INFO @ Tue, 02 Aug 2022 10:18:42: 14000000 INFO @ Tue, 02 Aug 2022 10:18:42: 6000000 INFO @ Tue, 02 Aug 2022 10:18:45: 10000000 INFO @ Tue, 02 Aug 2022 10:18:50: 15000000 INFO @ Tue, 02 Aug 2022 10:18:50: 7000000 INFO @ Tue, 02 Aug 2022 10:18:53: 11000000 INFO @ Tue, 02 Aug 2022 10:18:58: 16000000 INFO @ Tue, 02 Aug 2022 10:18:59: 8000000 INFO @ Tue, 02 Aug 2022 10:18:59: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:18:59: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:18:59: #1 total tags in treatment: 16108931 INFO @ Tue, 02 Aug 2022 10:18:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:18:59: #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 10:19:00: #1 tags after filtering in treatment: 16108931 INFO @ Tue, 02 Aug 2022 10:19:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:19:00: #1 finished! INFO @ Tue, 02 Aug 2022 10:19:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:19:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:19:01: #2 number of paired peaks: 220 WARNING @ Tue, 02 Aug 2022 10:19:01: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 02 Aug 2022 10:19:01: start model_add_line... INFO @ Tue, 02 Aug 2022 10:19:01: start X-correlation... INFO @ Tue, 02 Aug 2022 10:19:01: 12000000 INFO @ Tue, 02 Aug 2022 10:19:02: end of X-cor INFO @ Tue, 02 Aug 2022 10:19:02: #2 finished! INFO @ Tue, 02 Aug 2022 10:19:02: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 10:19:02: #2 alternative fragment length(s) may be 3,63,70 bps INFO @ Tue, 02 Aug 2022 10:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.05_model.r WARNING @ Tue, 02 Aug 2022 10:19:02: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:19:02: #2 You may need to consider one of the other alternative d(s): 3,63,70 WARNING @ Tue, 02 Aug 2022 10:19:02: #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 10:19:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:19:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:19:06: 9000000 INFO @ Tue, 02 Aug 2022 10:19:09: 13000000 INFO @ Tue, 02 Aug 2022 10:19:14: 10000000 INFO @ Tue, 02 Aug 2022 10:19:17: 14000000 INFO @ Tue, 02 Aug 2022 10:19:22: 11000000 INFO @ Tue, 02 Aug 2022 10:19:25: 15000000 INFO @ Tue, 02 Aug 2022 10:19:29: 12000000 INFO @ Tue, 02 Aug 2022 10:19:33: 16000000 INFO @ Tue, 02 Aug 2022 10:19:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:19:33: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:19:33: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:19:33: #1 total tags in treatment: 16108931 INFO @ Tue, 02 Aug 2022 10:19:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:19:33: #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 10:19:34: #1 tags after filtering in treatment: 16108931 INFO @ Tue, 02 Aug 2022 10:19:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:19:34: #1 finished! INFO @ Tue, 02 Aug 2022 10:19:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:19:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:19:35: #2 number of paired peaks: 220 WARNING @ Tue, 02 Aug 2022 10:19:35: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 02 Aug 2022 10:19:35: start model_add_line... INFO @ Tue, 02 Aug 2022 10:19:35: start X-correlation... INFO @ Tue, 02 Aug 2022 10:19:36: end of X-cor INFO @ Tue, 02 Aug 2022 10:19:36: #2 finished! INFO @ Tue, 02 Aug 2022 10:19:36: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 10:19:36: #2 alternative fragment length(s) may be 3,63,70 bps INFO @ Tue, 02 Aug 2022 10:19:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.10_model.r WARNING @ Tue, 02 Aug 2022 10:19:36: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:19:36: #2 You may need to consider one of the other alternative d(s): 3,63,70 WARNING @ Tue, 02 Aug 2022 10:19:36: #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 10:19:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:19:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:19:36: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:19:43: 14000000 INFO @ Tue, 02 Aug 2022 10:19:50: 15000000 INFO @ Tue, 02 Aug 2022 10:19:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:19:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:19:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.05_summits.bed INFO @ Tue, 02 Aug 2022 10:19:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (654 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:19:56: 16000000 INFO @ Tue, 02 Aug 2022 10:19:57: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:19:57: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:19:57: #1 total tags in treatment: 16108931 INFO @ Tue, 02 Aug 2022 10:19:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:19:57: #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 10:19:58: #1 tags after filtering in treatment: 16108931 INFO @ Tue, 02 Aug 2022 10:19:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:19:58: #1 finished! INFO @ Tue, 02 Aug 2022 10:19:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:19:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:19:59: #2 number of paired peaks: 220 WARNING @ Tue, 02 Aug 2022 10:19:59: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 02 Aug 2022 10:19:59: start model_add_line... INFO @ Tue, 02 Aug 2022 10:19:59: start X-correlation... INFO @ Tue, 02 Aug 2022 10:20:00: end of X-cor INFO @ Tue, 02 Aug 2022 10:20:00: #2 finished! INFO @ Tue, 02 Aug 2022 10:20:00: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 10:20:00: #2 alternative fragment length(s) may be 3,63,70 bps INFO @ Tue, 02 Aug 2022 10:20:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.20_model.r WARNING @ Tue, 02 Aug 2022 10:20:00: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:20:00: #2 You may need to consider one of the other alternative d(s): 3,63,70 WARNING @ Tue, 02 Aug 2022 10:20:00: #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 10:20:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:20:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:20:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:20:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:20:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:20:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.10_summits.bed INFO @ Tue, 02 Aug 2022 10:20:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (421 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:20:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:20:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:20:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:20:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435521/SRX10435521.20_summits.bed INFO @ Tue, 02 Aug 2022 10:20:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 41 millis CompletedMACS2peakCalling