Job ID = 14159153 SRX = SRX9120612 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 29658545 spots for SRR12638555/SRR12638555.sra Written 29658545 spots for SRR12638555/SRR12638555.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159412 ("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: 00:07:43 29658545 reads; of these: 29658545 (100.00%) were unpaired; of these: 1609094 (5.43%) aligned 0 times 23267105 (78.45%) aligned exactly 1 time 4782346 (16.12%) aligned >1 times 94.57% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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] 6075492 / 28049451 = 0.2166 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 20:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.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 @ Wed, 08 Dec 2021 20:12:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:12:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:12:28: 1000000 INFO @ Wed, 08 Dec 2021 20:12:36: 2000000 INFO @ Wed, 08 Dec 2021 20:12:45: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 20:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.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 @ Wed, 08 Dec 2021 20:12:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:12:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:12:53: 4000000 INFO @ Wed, 08 Dec 2021 20:12:57: 1000000 INFO @ Wed, 08 Dec 2021 20:13:04: 5000000 INFO @ Wed, 08 Dec 2021 20:13:06: 2000000 INFO @ Wed, 08 Dec 2021 20:13:14: 6000000 INFO @ Wed, 08 Dec 2021 20:13:14: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 20:13:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.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 @ Wed, 08 Dec 2021 20:13:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:13:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:13:22: 4000000 INFO @ Wed, 08 Dec 2021 20:13:24: 7000000 INFO @ Wed, 08 Dec 2021 20:13:28: 1000000 INFO @ Wed, 08 Dec 2021 20:13:30: 5000000 INFO @ Wed, 08 Dec 2021 20:13:35: 8000000 INFO @ Wed, 08 Dec 2021 20:13:37: 2000000 INFO @ Wed, 08 Dec 2021 20:13:38: 6000000 INFO @ Wed, 08 Dec 2021 20:13:46: 3000000 INFO @ Wed, 08 Dec 2021 20:13:46: 9000000 INFO @ Wed, 08 Dec 2021 20:13:46: 7000000 INFO @ Wed, 08 Dec 2021 20:13:54: 8000000 INFO @ Wed, 08 Dec 2021 20:13:55: 4000000 INFO @ Wed, 08 Dec 2021 20:13:57: 10000000 INFO @ Wed, 08 Dec 2021 20:14:03: 9000000 INFO @ Wed, 08 Dec 2021 20:14:04: 5000000 INFO @ Wed, 08 Dec 2021 20:14:08: 11000000 INFO @ Wed, 08 Dec 2021 20:14:11: 10000000 INFO @ Wed, 08 Dec 2021 20:14:13: 6000000 INFO @ Wed, 08 Dec 2021 20:14:18: 12000000 INFO @ Wed, 08 Dec 2021 20:14:19: 11000000 INFO @ Wed, 08 Dec 2021 20:14:22: 7000000 INFO @ Wed, 08 Dec 2021 20:14:27: 12000000 INFO @ Wed, 08 Dec 2021 20:14:29: 13000000 INFO @ Wed, 08 Dec 2021 20:14:31: 8000000 INFO @ Wed, 08 Dec 2021 20:14:35: 13000000 INFO @ Wed, 08 Dec 2021 20:14:39: 14000000 INFO @ Wed, 08 Dec 2021 20:14:40: 9000000 INFO @ Wed, 08 Dec 2021 20:14:43: 14000000 INFO @ Wed, 08 Dec 2021 20:14:48: 10000000 INFO @ Wed, 08 Dec 2021 20:14:49: 15000000 INFO @ Wed, 08 Dec 2021 20:14:51: 15000000 INFO @ Wed, 08 Dec 2021 20:14:58: 11000000 INFO @ Wed, 08 Dec 2021 20:14:59: 16000000 INFO @ Wed, 08 Dec 2021 20:15:00: 16000000 INFO @ Wed, 08 Dec 2021 20:15:06: 12000000 INFO @ Wed, 08 Dec 2021 20:15:08: 17000000 INFO @ Wed, 08 Dec 2021 20:15:10: 17000000 INFO @ Wed, 08 Dec 2021 20:15:15: 13000000 INFO @ Wed, 08 Dec 2021 20:15:15: 18000000 INFO @ Wed, 08 Dec 2021 20:15:20: 18000000 INFO @ Wed, 08 Dec 2021 20:15:23: 19000000 INFO @ Wed, 08 Dec 2021 20:15:23: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:15:30: 19000000 INFO @ Wed, 08 Dec 2021 20:15:31: 20000000 INFO @ Wed, 08 Dec 2021 20:15:32: 15000000 INFO @ Wed, 08 Dec 2021 20:15:38: 21000000 INFO @ Wed, 08 Dec 2021 20:15:40: 16000000 INFO @ Wed, 08 Dec 2021 20:15:40: 20000000 INFO @ Wed, 08 Dec 2021 20:15:46: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:15:46: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:15:46: #1 total tags in treatment: 21973959 INFO @ Wed, 08 Dec 2021 20:15:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:15:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:15:46: #1 tags after filtering in treatment: 21973959 INFO @ Wed, 08 Dec 2021 20:15:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:15:46: #1 finished! INFO @ Wed, 08 Dec 2021 20:15:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:15:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:15:48: #2 number of paired peaks: 192 WARNING @ Wed, 08 Dec 2021 20:15:48: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Wed, 08 Dec 2021 20:15:48: start model_add_line... INFO @ Wed, 08 Dec 2021 20:15:48: start X-correlation... INFO @ Wed, 08 Dec 2021 20:15:48: end of X-cor INFO @ Wed, 08 Dec 2021 20:15:48: #2 finished! INFO @ Wed, 08 Dec 2021 20:15:48: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:15:48: #2 alternative fragment length(s) may be 1,38,535,547 bps INFO @ Wed, 08 Dec 2021 20:15:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.10_model.r WARNING @ Wed, 08 Dec 2021 20:15:48: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:15:48: #2 You may need to consider one of the other alternative d(s): 1,38,535,547 WARNING @ Wed, 08 Dec 2021 20:15:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:15:48: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:15:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:15:49: 17000000 INFO @ Wed, 08 Dec 2021 20:15:50: 21000000 INFO @ Wed, 08 Dec 2021 20:15:57: 18000000 INFO @ Wed, 08 Dec 2021 20:16:00: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:16:00: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:16:00: #1 total tags in treatment: 21973959 INFO @ Wed, 08 Dec 2021 20:16:00: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:16:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:16:00: #1 tags after filtering in treatment: 21973959 INFO @ Wed, 08 Dec 2021 20:16:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:16:00: #1 finished! INFO @ Wed, 08 Dec 2021 20:16:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:16:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:16:02: #2 number of paired peaks: 192 WARNING @ Wed, 08 Dec 2021 20:16:02: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Wed, 08 Dec 2021 20:16:02: start model_add_line... INFO @ Wed, 08 Dec 2021 20:16:02: start X-correlation... INFO @ Wed, 08 Dec 2021 20:16:02: end of X-cor INFO @ Wed, 08 Dec 2021 20:16:02: #2 finished! INFO @ Wed, 08 Dec 2021 20:16:02: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:16:02: #2 alternative fragment length(s) may be 1,38,535,547 bps INFO @ Wed, 08 Dec 2021 20:16:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.05_model.r WARNING @ Wed, 08 Dec 2021 20:16:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:16:02: #2 You may need to consider one of the other alternative d(s): 1,38,535,547 WARNING @ Wed, 08 Dec 2021 20:16:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:16:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:16:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:16:05: 19000000 INFO @ Wed, 08 Dec 2021 20:16:13: 20000000 INFO @ Wed, 08 Dec 2021 20:16:21: 21000000 INFO @ Wed, 08 Dec 2021 20:16:29: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:16:29: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:16:29: #1 total tags in treatment: 21973959 INFO @ Wed, 08 Dec 2021 20:16:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:16:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:16:29: #1 tags after filtering in treatment: 21973959 INFO @ Wed, 08 Dec 2021 20:16:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:16:29: #1 finished! INFO @ Wed, 08 Dec 2021 20:16:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:16:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:16:31: #2 number of paired peaks: 192 WARNING @ Wed, 08 Dec 2021 20:16:31: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Wed, 08 Dec 2021 20:16:31: start model_add_line... INFO @ Wed, 08 Dec 2021 20:16:31: start X-correlation... INFO @ Wed, 08 Dec 2021 20:16:31: end of X-cor INFO @ Wed, 08 Dec 2021 20:16:31: #2 finished! INFO @ Wed, 08 Dec 2021 20:16:31: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:16:31: #2 alternative fragment length(s) may be 1,38,535,547 bps INFO @ Wed, 08 Dec 2021 20:16:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.20_model.r WARNING @ Wed, 08 Dec 2021 20:16:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:16:31: #2 You may need to consider one of the other alternative d(s): 1,38,535,547 WARNING @ Wed, 08 Dec 2021 20:16:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:16:31: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:16:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:16:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:16:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:16:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:16:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:16:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.10_summits.bed INFO @ Wed, 08 Dec 2021 20:16:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:17:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:17:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:17:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.05_summits.bed INFO @ Wed, 08 Dec 2021 20:17:10: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:17:18: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:17:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:17:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:17:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.20_summits.bed INFO @ Wed, 08 Dec 2021 20:17:39: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling