Job ID = 16432403 SRX = SRX15407785 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 'SRR19348965'... 2022-08-02T00:32:11 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:33:04 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:33:05 prefetch.2.10.7: 'SRR19348965' is valid 2022-08-02T00:33:05 prefetch.2.10.7: 1) 'SRR19348965' was downloaded successfully 2022-08-02T00:33:05 prefetch.2.10.7: 'SRR19348965' has 0 unresolved dependencies Read 19285694 spots for SRR19348965/SRR19348965.sra Written 19285694 spots for SRR19348965/SRR19348965.sra fastq に変換しました。 bowtie でマッピング中... Your job 16433761 ("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: 00:06:00 19285694 reads; of these: 19285694 (100.00%) were unpaired; of these: 1098427 (5.70%) aligned 0 times 15578772 (80.78%) aligned exactly 1 time 2608495 (13.53%) aligned >1 times 94.30% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 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] 2153258 / 18187267 = 0.1184 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 09:46:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.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 09:46:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:46:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:46:34: 1000000 INFO @ Tue, 02 Aug 2022 09:46:41: 2000000 INFO @ Tue, 02 Aug 2022 09:46:47: 3000000 INFO @ Tue, 02 Aug 2022 09:46:54: 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 09:46:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.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 09:46:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:46:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:47:01: 5000000 INFO @ Tue, 02 Aug 2022 09:47:04: 1000000 INFO @ Tue, 02 Aug 2022 09:47:08: 6000000 INFO @ Tue, 02 Aug 2022 09:47:09: 2000000 INFO @ Tue, 02 Aug 2022 09:47:15: 7000000 INFO @ Tue, 02 Aug 2022 09:47:15: 3000000 INFO @ Tue, 02 Aug 2022 09:47:21: 4000000 INFO @ Tue, 02 Aug 2022 09:47:22: 8000000 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 09:47:27: 5000000 INFO @ Tue, 02 Aug 2022 09:47:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.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 09:47:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:47:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:47:29: 9000000 INFO @ Tue, 02 Aug 2022 09:47:33: 6000000 INFO @ Tue, 02 Aug 2022 09:47:36: 1000000 INFO @ Tue, 02 Aug 2022 09:47:37: 10000000 INFO @ Tue, 02 Aug 2022 09:47:39: 7000000 INFO @ Tue, 02 Aug 2022 09:47:43: 2000000 INFO @ Tue, 02 Aug 2022 09:47:44: 11000000 INFO @ Tue, 02 Aug 2022 09:47:45: 8000000 INFO @ Tue, 02 Aug 2022 09:47:51: 3000000 INFO @ Tue, 02 Aug 2022 09:47:52: 9000000 INFO @ Tue, 02 Aug 2022 09:47:52: 12000000 INFO @ Tue, 02 Aug 2022 09:47:58: 10000000 INFO @ Tue, 02 Aug 2022 09:47:59: 4000000 INFO @ Tue, 02 Aug 2022 09:47:59: 13000000 INFO @ Tue, 02 Aug 2022 09:48:04: 11000000 INFO @ Tue, 02 Aug 2022 09:48:06: 5000000 INFO @ Tue, 02 Aug 2022 09:48:06: 14000000 INFO @ Tue, 02 Aug 2022 09:48:11: 12000000 INFO @ Tue, 02 Aug 2022 09:48:14: 6000000 INFO @ Tue, 02 Aug 2022 09:48:14: 15000000 INFO @ Tue, 02 Aug 2022 09:48:18: 13000000 INFO @ Tue, 02 Aug 2022 09:48:21: 16000000 INFO @ Tue, 02 Aug 2022 09:48:21: 7000000 INFO @ Tue, 02 Aug 2022 09:48:21: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:48:21: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:48:21: #1 total tags in treatment: 16034009 INFO @ Tue, 02 Aug 2022 09:48:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:48:21: #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 09:48:22: #1 tags after filtering in treatment: 16034009 INFO @ Tue, 02 Aug 2022 09:48:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:48:22: #1 finished! INFO @ Tue, 02 Aug 2022 09:48:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:48:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:48:23: #2 number of paired peaks: 181 WARNING @ Tue, 02 Aug 2022 09:48:23: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 02 Aug 2022 09:48:23: start model_add_line... INFO @ Tue, 02 Aug 2022 09:48:23: start X-correlation... INFO @ Tue, 02 Aug 2022 09:48:23: end of X-cor INFO @ Tue, 02 Aug 2022 09:48:23: #2 finished! INFO @ Tue, 02 Aug 2022 09:48:23: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 09:48:23: #2 alternative fragment length(s) may be 2,71 bps INFO @ Tue, 02 Aug 2022 09:48:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.05_model.r WARNING @ Tue, 02 Aug 2022 09:48:23: #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 09:48:23: #2 You may need to consider one of the other alternative d(s): 2,71 WARNING @ Tue, 02 Aug 2022 09:48:23: #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 09:48:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:48:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:48:25: 14000000 INFO @ Tue, 02 Aug 2022 09:48:29: 8000000 INFO @ Tue, 02 Aug 2022 09:48:31: 15000000 INFO @ Tue, 02 Aug 2022 09:48:36: 9000000 INFO @ Tue, 02 Aug 2022 09:48:37: 16000000 INFO @ Tue, 02 Aug 2022 09:48:37: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:48:37: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:48:37: #1 total tags in treatment: 16034009 INFO @ Tue, 02 Aug 2022 09:48:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:48:37: #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 09:48:37: #1 tags after filtering in treatment: 16034009 INFO @ Tue, 02 Aug 2022 09:48:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:48:37: #1 finished! INFO @ Tue, 02 Aug 2022 09:48:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:48:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:48:38: #2 number of paired peaks: 181 WARNING @ Tue, 02 Aug 2022 09:48:38: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 02 Aug 2022 09:48:38: start model_add_line... INFO @ Tue, 02 Aug 2022 09:48:38: start X-correlation... INFO @ Tue, 02 Aug 2022 09:48:38: end of X-cor INFO @ Tue, 02 Aug 2022 09:48:38: #2 finished! INFO @ Tue, 02 Aug 2022 09:48:38: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 09:48:38: #2 alternative fragment length(s) may be 2,71 bps INFO @ Tue, 02 Aug 2022 09:48:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.10_model.r WARNING @ Tue, 02 Aug 2022 09:48:39: #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 09:48:39: #2 You may need to consider one of the other alternative d(s): 2,71 WARNING @ Tue, 02 Aug 2022 09:48:39: #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 09:48:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:48:43: 10000000 INFO @ Tue, 02 Aug 2022 09:48:50: 11000000 INFO @ Tue, 02 Aug 2022 09:48:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:48:58: 12000000 INFO @ Tue, 02 Aug 2022 09:49:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:49:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:49:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.05_summits.bed INFO @ Tue, 02 Aug 2022 09:49:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1129 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:49:05: 13000000 INFO @ Tue, 02 Aug 2022 09:49:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:49:12: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:49:18: 15000000 INFO @ Tue, 02 Aug 2022 09:49:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:49:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:49:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.10_summits.bed INFO @ Tue, 02 Aug 2022 09:49:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (482 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:49:25: 16000000 INFO @ Tue, 02 Aug 2022 09:49:25: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:49:25: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:49:25: #1 total tags in treatment: 16034009 INFO @ Tue, 02 Aug 2022 09:49:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:49:25: #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 09:49:26: #1 tags after filtering in treatment: 16034009 INFO @ Tue, 02 Aug 2022 09:49:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:49:26: #1 finished! INFO @ Tue, 02 Aug 2022 09:49:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:49:27: #2 number of paired peaks: 181 WARNING @ Tue, 02 Aug 2022 09:49:27: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 02 Aug 2022 09:49:27: start model_add_line... INFO @ Tue, 02 Aug 2022 09:49:27: start X-correlation... INFO @ Tue, 02 Aug 2022 09:49:27: end of X-cor INFO @ Tue, 02 Aug 2022 09:49:27: #2 finished! INFO @ Tue, 02 Aug 2022 09:49:27: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 09:49:27: #2 alternative fragment length(s) may be 2,71 bps INFO @ Tue, 02 Aug 2022 09:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.20_model.r WARNING @ Tue, 02 Aug 2022 09:49:27: #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 09:49:27: #2 You may need to consider one of the other alternative d(s): 2,71 WARNING @ Tue, 02 Aug 2022 09:49:27: #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 09:49:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:49:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:50:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:50:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:50:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407785/SRX15407785.20_summits.bed INFO @ Tue, 02 Aug 2022 09:50:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (212 records, 4 fields): 18 millis CompletedMACS2peakCalling