Job ID = 10165777 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 10166081 ("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: 00:06:39 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: 00:06:39 Overall time: 00:06:39 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:03:20: # 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 @ Thu, 08 Oct 2020 20:03:20: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:03:20: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:03:25: 1000000 INFO @ Thu, 08 Oct 2020 20:03:30: 2000000 INFO @ Thu, 08 Oct 2020 20:03:36: 3000000 INFO @ Thu, 08 Oct 2020 20:03:41: 4000000 INFO @ Thu, 08 Oct 2020 20:03:46: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:03:50: # 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 @ Thu, 08 Oct 2020 20:03:50: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:03:50: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:03:51: 6000000 INFO @ Thu, 08 Oct 2020 20:03:56: 1000000 INFO @ Thu, 08 Oct 2020 20:03:57: 7000000 INFO @ Thu, 08 Oct 2020 20:04:02: 2000000 INFO @ Thu, 08 Oct 2020 20:04:03: 8000000 INFO @ Thu, 08 Oct 2020 20:04:08: 3000000 INFO @ Thu, 08 Oct 2020 20:04:09: 9000000 INFO @ Thu, 08 Oct 2020 20:04:13: 4000000 INFO @ Thu, 08 Oct 2020 20:04:14: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:04:19: 5000000 INFO @ Thu, 08 Oct 2020 20:04:20: # 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 @ Thu, 08 Oct 2020 20:04:20: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:20: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:20: 11000000 INFO @ Thu, 08 Oct 2020 20:04:25: 6000000 INFO @ Thu, 08 Oct 2020 20:04:26: 12000000 INFO @ Thu, 08 Oct 2020 20:04:26: 1000000 INFO @ Thu, 08 Oct 2020 20:04:31: 7000000 INFO @ Thu, 08 Oct 2020 20:04:32: 13000000 INFO @ Thu, 08 Oct 2020 20:04:32: 2000000 INFO @ Thu, 08 Oct 2020 20:04:37: 8000000 INFO @ Thu, 08 Oct 2020 20:04:37: 14000000 INFO @ Thu, 08 Oct 2020 20:04:38: 3000000 INFO @ Thu, 08 Oct 2020 20:04:43: 9000000 INFO @ Thu, 08 Oct 2020 20:04:43: 15000000 INFO @ Thu, 08 Oct 2020 20:04:44: 4000000 INFO @ Thu, 08 Oct 2020 20:04:48: 10000000 INFO @ Thu, 08 Oct 2020 20:04:49: 16000000 INFO @ Thu, 08 Oct 2020 20:04:50: 5000000 INFO @ Thu, 08 Oct 2020 20:04:54: 11000000 INFO @ Thu, 08 Oct 2020 20:04:55: 17000000 INFO @ Thu, 08 Oct 2020 20:04:56: 6000000 INFO @ Thu, 08 Oct 2020 20:05:00: 12000000 INFO @ Thu, 08 Oct 2020 20:05:00: 18000000 INFO @ Thu, 08 Oct 2020 20:05:01: 7000000 INFO @ Thu, 08 Oct 2020 20:05:06: 13000000 INFO @ Thu, 08 Oct 2020 20:05:06: 19000000 INFO @ Thu, 08 Oct 2020 20:05:07: 8000000 INFO @ Thu, 08 Oct 2020 20:05:12: 14000000 INFO @ Thu, 08 Oct 2020 20:05:12: 20000000 INFO @ Thu, 08 Oct 2020 20:05:13: 9000000 INFO @ Thu, 08 Oct 2020 20:05:17: 15000000 INFO @ Thu, 08 Oct 2020 20:05:18: 21000000 INFO @ Thu, 08 Oct 2020 20:05:19: 10000000 INFO @ Thu, 08 Oct 2020 20:05:23: 16000000 INFO @ Thu, 08 Oct 2020 20:05:23: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:05:23: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:05:23: #1 total tags in treatment: 21973959 INFO @ Thu, 08 Oct 2020 20:05:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:05:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:05:24: #1 tags after filtering in treatment: 21973959 INFO @ Thu, 08 Oct 2020 20:05:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:05:24: #1 finished! INFO @ Thu, 08 Oct 2020 20:05:24: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:05:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:05:25: 11000000 INFO @ Thu, 08 Oct 2020 20:05:25: #2 number of paired peaks: 192 WARNING @ Thu, 08 Oct 2020 20:05:25: 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 @ Thu, 08 Oct 2020 20:05:25: start model_add_line... INFO @ Thu, 08 Oct 2020 20:05:25: start X-correlation... INFO @ Thu, 08 Oct 2020 20:05:25: end of X-cor INFO @ Thu, 08 Oct 2020 20:05:25: #2 finished! INFO @ Thu, 08 Oct 2020 20:05:25: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:05:25: #2 alternative fragment length(s) may be 1,38,535,547 bps INFO @ Thu, 08 Oct 2020 20:05:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.05_model.r WARNING @ Thu, 08 Oct 2020 20:05:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:05:25: #2 You may need to consider one of the other alternative d(s): 1,38,535,547 WARNING @ Thu, 08 Oct 2020 20:05:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:05:25: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:05:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:05:29: 17000000 INFO @ Thu, 08 Oct 2020 20:05:31: 12000000 INFO @ Thu, 08 Oct 2020 20:05:34: 18000000 INFO @ Thu, 08 Oct 2020 20:05:36: 13000000 INFO @ Thu, 08 Oct 2020 20:05:40: 19000000 INFO @ Thu, 08 Oct 2020 20:05:42: 14000000 INFO @ Thu, 08 Oct 2020 20:05:46: 20000000 INFO @ Thu, 08 Oct 2020 20:05:48: 15000000 INFO @ Thu, 08 Oct 2020 20:05:51: 21000000 INFO @ Thu, 08 Oct 2020 20:05:53: 16000000 INFO @ Thu, 08 Oct 2020 20:05:57: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:05:57: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:05:57: #1 total tags in treatment: 21973959 INFO @ Thu, 08 Oct 2020 20:05:57: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:05:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:05:57: #1 tags after filtering in treatment: 21973959 INFO @ Thu, 08 Oct 2020 20:05:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:05:57: #1 finished! INFO @ Thu, 08 Oct 2020 20:05:57: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:05:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:05:59: #2 number of paired peaks: 192 WARNING @ Thu, 08 Oct 2020 20:05:59: 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 @ Thu, 08 Oct 2020 20:05:59: start model_add_line... INFO @ Thu, 08 Oct 2020 20:05:59: start X-correlation... INFO @ Thu, 08 Oct 2020 20:05:59: end of X-cor INFO @ Thu, 08 Oct 2020 20:05:59: #2 finished! INFO @ Thu, 08 Oct 2020 20:05:59: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:05:59: #2 alternative fragment length(s) may be 1,38,535,547 bps INFO @ Thu, 08 Oct 2020 20:05:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.10_model.r WARNING @ Thu, 08 Oct 2020 20:05:59: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:05:59: #2 You may need to consider one of the other alternative d(s): 1,38,535,547 WARNING @ Thu, 08 Oct 2020 20:05:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:05:59: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:05:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:05:59: 17000000 INFO @ Thu, 08 Oct 2020 20:06:00: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:06:05: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:06:10: 19000000 INFO @ Thu, 08 Oct 2020 20:06:15: 20000000 INFO @ Thu, 08 Oct 2020 20:06:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:06:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:06:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.05_summits.bed INFO @ Thu, 08 Oct 2020 20:06:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:06:21: 21000000 INFO @ Thu, 08 Oct 2020 20:06:26: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:26: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:26: #1 total tags in treatment: 21973959 INFO @ Thu, 08 Oct 2020 20:06:26: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:06:26: #1 tags after filtering in treatment: 21973959 INFO @ Thu, 08 Oct 2020 20:06:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:26: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:26: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:28: #2 number of paired peaks: 192 WARNING @ Thu, 08 Oct 2020 20:06:28: 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 @ Thu, 08 Oct 2020 20:06:28: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:28: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:28: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:28: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:28: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:06:28: #2 alternative fragment length(s) may be 1,38,535,547 bps INFO @ Thu, 08 Oct 2020 20:06:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.20_model.r WARNING @ Thu, 08 Oct 2020 20:06:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:06:28: #2 You may need to consider one of the other alternative d(s): 1,38,535,547 WARNING @ Thu, 08 Oct 2020 20:06:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:06:28: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:33: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:06:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:06:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:06:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.10_summits.bed INFO @ Thu, 08 Oct 2020 20:06:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:07:01: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120612/SRX9120612.20_summits.bed INFO @ Thu, 08 Oct 2020 20:07:17: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling