Job ID = 14168659 SRX = ERX3978872 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23864185 spots for ERR3975941/ERR3975941.sra Written 23864185 spots for ERR3975941/ERR3975941.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169905 ("srTdm6") 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: 02:05:45 23864185 reads; of these: 23864185 (100.00%) were paired; of these: 4882929 (20.46%) aligned concordantly 0 times 10750353 (45.05%) aligned concordantly exactly 1 time 8230903 (34.49%) aligned concordantly >1 times ---- 4882929 pairs aligned concordantly 0 times; of these: 588274 (12.05%) aligned discordantly 1 time ---- 4294655 pairs aligned 0 times concordantly or discordantly; of these: 8589310 mates make up the pairs; of these: 3872017 (45.08%) aligned 0 times 1476926 (17.19%) aligned exactly 1 time 3240367 (37.73%) aligned >1 times 91.89% overall alignment rate Time searching: 02:05:45 Overall time: 02:05:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 5399092 / 19324446 = 0.2794 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 @ Fri, 10 Dec 2021 21:34:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 21:34:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:34:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:34:30: 1000000 INFO @ Fri, 10 Dec 2021 21:34:34: 2000000 INFO @ Fri, 10 Dec 2021 21:34:39: 3000000 INFO @ Fri, 10 Dec 2021 21:34:44: 4000000 INFO @ Fri, 10 Dec 2021 21:34:49: 5000000 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 @ Fri, 10 Dec 2021 21:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 21:34:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:34:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:34:53: 6000000 INFO @ Fri, 10 Dec 2021 21:34:58: 7000000 INFO @ Fri, 10 Dec 2021 21:34:59: 1000000 INFO @ Fri, 10 Dec 2021 21:35:03: 8000000 INFO @ Fri, 10 Dec 2021 21:35:05: 2000000 INFO @ Fri, 10 Dec 2021 21:35:08: 9000000 INFO @ Fri, 10 Dec 2021 21:35:11: 3000000 INFO @ Fri, 10 Dec 2021 21:35:13: 10000000 INFO @ Fri, 10 Dec 2021 21:35:16: 4000000 INFO @ Fri, 10 Dec 2021 21:35:18: 11000000 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 @ Fri, 10 Dec 2021 21:35:22: 5000000 INFO @ Fri, 10 Dec 2021 21:35:23: 12000000 INFO @ Fri, 10 Dec 2021 21:35:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 21:35:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:35:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:35:28: 6000000 INFO @ Fri, 10 Dec 2021 21:35:28: 13000000 INFO @ Fri, 10 Dec 2021 21:35:29: 1000000 INFO @ Fri, 10 Dec 2021 21:35:33: 14000000 INFO @ Fri, 10 Dec 2021 21:35:34: 7000000 INFO @ Fri, 10 Dec 2021 21:35:35: 2000000 INFO @ Fri, 10 Dec 2021 21:35:38: 15000000 INFO @ Fri, 10 Dec 2021 21:35:40: 8000000 INFO @ Fri, 10 Dec 2021 21:35:41: 3000000 INFO @ Fri, 10 Dec 2021 21:35:43: 16000000 INFO @ Fri, 10 Dec 2021 21:35:46: 9000000 INFO @ Fri, 10 Dec 2021 21:35:47: 4000000 INFO @ Fri, 10 Dec 2021 21:35:48: 17000000 INFO @ Fri, 10 Dec 2021 21:35:52: 10000000 INFO @ Fri, 10 Dec 2021 21:35:53: 18000000 INFO @ Fri, 10 Dec 2021 21:35:53: 5000000 INFO @ Fri, 10 Dec 2021 21:35:58: 11000000 INFO @ Fri, 10 Dec 2021 21:35:58: 19000000 INFO @ Fri, 10 Dec 2021 21:35:59: 6000000 INFO @ Fri, 10 Dec 2021 21:36:03: 20000000 INFO @ Fri, 10 Dec 2021 21:36:04: 12000000 INFO @ Fri, 10 Dec 2021 21:36:06: 7000000 INFO @ Fri, 10 Dec 2021 21:36:08: 21000000 INFO @ Fri, 10 Dec 2021 21:36:10: 13000000 INFO @ Fri, 10 Dec 2021 21:36:12: 8000000 INFO @ Fri, 10 Dec 2021 21:36:13: 22000000 INFO @ Fri, 10 Dec 2021 21:36:16: 14000000 INFO @ Fri, 10 Dec 2021 21:36:18: 9000000 INFO @ Fri, 10 Dec 2021 21:36:18: 23000000 INFO @ Fri, 10 Dec 2021 21:36:22: 15000000 INFO @ Fri, 10 Dec 2021 21:36:23: 24000000 INFO @ Fri, 10 Dec 2021 21:36:24: 10000000 INFO @ Fri, 10 Dec 2021 21:36:28: 25000000 INFO @ Fri, 10 Dec 2021 21:36:28: 16000000 INFO @ Fri, 10 Dec 2021 21:36:30: 11000000 INFO @ Fri, 10 Dec 2021 21:36:33: 26000000 INFO @ Fri, 10 Dec 2021 21:36:34: 17000000 INFO @ Fri, 10 Dec 2021 21:36:36: 12000000 INFO @ Fri, 10 Dec 2021 21:36:37: 27000000 INFO @ Fri, 10 Dec 2021 21:36:40: 18000000 INFO @ Fri, 10 Dec 2021 21:36:42: 13000000 INFO @ Fri, 10 Dec 2021 21:36:42: 28000000 INFO @ Fri, 10 Dec 2021 21:36:46: 19000000 INFO @ Fri, 10 Dec 2021 21:36:47: 29000000 INFO @ Fri, 10 Dec 2021 21:36:48: 14000000 INFO @ Fri, 10 Dec 2021 21:36:52: 30000000 INFO @ Fri, 10 Dec 2021 21:36:52: 20000000 INFO @ Fri, 10 Dec 2021 21:36:54: 15000000 INFO @ Fri, 10 Dec 2021 21:36:57: 31000000 INFO @ Fri, 10 Dec 2021 21:36:58: 21000000 INFO @ Fri, 10 Dec 2021 21:37:00: 16000000 INFO @ Fri, 10 Dec 2021 21:37:02: 32000000 INFO @ Fri, 10 Dec 2021 21:37:04: 22000000 INFO @ Fri, 10 Dec 2021 21:37:06: 17000000 INFO @ Fri, 10 Dec 2021 21:37:07: 33000000 INFO @ Fri, 10 Dec 2021 21:37:07: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:37:07: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:37:07: #1 total tags in treatment: 13645888 INFO @ Fri, 10 Dec 2021 21:37:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:37:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:37:07: #1 tags after filtering in treatment: 12040082 INFO @ Fri, 10 Dec 2021 21:37:07: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 21:37:07: #1 finished! INFO @ Fri, 10 Dec 2021 21:37:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:37:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:37:08: #2 number of paired peaks: 402 WARNING @ Fri, 10 Dec 2021 21:37:08: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Fri, 10 Dec 2021 21:37:08: start model_add_line... INFO @ Fri, 10 Dec 2021 21:37:08: start X-correlation... INFO @ Fri, 10 Dec 2021 21:37:08: end of X-cor INFO @ Fri, 10 Dec 2021 21:37:08: #2 finished! INFO @ Fri, 10 Dec 2021 21:37:08: #2 predicted fragment length is 126 bps INFO @ Fri, 10 Dec 2021 21:37:08: #2 alternative fragment length(s) may be 126 bps INFO @ Fri, 10 Dec 2021 21:37:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.05_model.r WARNING @ Fri, 10 Dec 2021 21:37:08: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:37:08: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Fri, 10 Dec 2021 21:37:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:37:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:37:10: 23000000 INFO @ Fri, 10 Dec 2021 21:37:12: 18000000 INFO @ Fri, 10 Dec 2021 21:37:16: 24000000 INFO @ Fri, 10 Dec 2021 21:37:17: 19000000 INFO @ Fri, 10 Dec 2021 21:37:22: 25000000 INFO @ Fri, 10 Dec 2021 21:37:23: 20000000 INFO @ Fri, 10 Dec 2021 21:37:27: 26000000 INFO @ Fri, 10 Dec 2021 21:37:29: 21000000 INFO @ Fri, 10 Dec 2021 21:37:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:37:33: 27000000 INFO @ Fri, 10 Dec 2021 21:37:35: 22000000 INFO @ Fri, 10 Dec 2021 21:37:39: 28000000 INFO @ Fri, 10 Dec 2021 21:37:41: 23000000 INFO @ Fri, 10 Dec 2021 21:37:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:37:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:37:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.05_summits.bed INFO @ Fri, 10 Dec 2021 21:37:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6304 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:37:44: 29000000 INFO @ Fri, 10 Dec 2021 21:37:47: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:37:50: 30000000 INFO @ Fri, 10 Dec 2021 21:37:52: 25000000 INFO @ Fri, 10 Dec 2021 21:37:56: 31000000 INFO @ Fri, 10 Dec 2021 21:37:58: 26000000 INFO @ Fri, 10 Dec 2021 21:38:01: 32000000 INFO @ Fri, 10 Dec 2021 21:38:04: 27000000 INFO @ Fri, 10 Dec 2021 21:38:07: 33000000 INFO @ Fri, 10 Dec 2021 21:38:08: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:38:08: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:38:08: #1 total tags in treatment: 13645888 INFO @ Fri, 10 Dec 2021 21:38:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:38:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:38:08: #1 tags after filtering in treatment: 12040082 INFO @ Fri, 10 Dec 2021 21:38:08: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 21:38:08: #1 finished! INFO @ Fri, 10 Dec 2021 21:38:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:38:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:38:09: #2 number of paired peaks: 402 WARNING @ Fri, 10 Dec 2021 21:38:09: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Fri, 10 Dec 2021 21:38:09: start model_add_line... INFO @ Fri, 10 Dec 2021 21:38:09: start X-correlation... INFO @ Fri, 10 Dec 2021 21:38:09: end of X-cor INFO @ Fri, 10 Dec 2021 21:38:09: #2 finished! INFO @ Fri, 10 Dec 2021 21:38:09: #2 predicted fragment length is 126 bps INFO @ Fri, 10 Dec 2021 21:38:09: #2 alternative fragment length(s) may be 126 bps INFO @ Fri, 10 Dec 2021 21:38:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.10_model.r WARNING @ Fri, 10 Dec 2021 21:38:09: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:38:09: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Fri, 10 Dec 2021 21:38:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:38:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:38:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:38:10: 28000000 INFO @ Fri, 10 Dec 2021 21:38:15: 29000000 INFO @ Fri, 10 Dec 2021 21:38:21: 30000000 INFO @ Fri, 10 Dec 2021 21:38:26: 31000000 INFO @ Fri, 10 Dec 2021 21:38:32: 32000000 INFO @ Fri, 10 Dec 2021 21:38:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:38:38: 33000000 INFO @ Fri, 10 Dec 2021 21:38:38: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:38:38: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:38:38: #1 total tags in treatment: 13645888 INFO @ Fri, 10 Dec 2021 21:38:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:38:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:38:38: #1 tags after filtering in treatment: 12040082 INFO @ Fri, 10 Dec 2021 21:38:38: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 21:38:38: #1 finished! INFO @ Fri, 10 Dec 2021 21:38:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:38:39: #2 number of paired peaks: 402 WARNING @ Fri, 10 Dec 2021 21:38:39: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Fri, 10 Dec 2021 21:38:39: start model_add_line... INFO @ Fri, 10 Dec 2021 21:38:39: start X-correlation... INFO @ Fri, 10 Dec 2021 21:38:39: end of X-cor INFO @ Fri, 10 Dec 2021 21:38:39: #2 finished! INFO @ Fri, 10 Dec 2021 21:38:39: #2 predicted fragment length is 126 bps INFO @ Fri, 10 Dec 2021 21:38:39: #2 alternative fragment length(s) may be 126 bps INFO @ Fri, 10 Dec 2021 21:38:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.20_model.r WARNING @ Fri, 10 Dec 2021 21:38:39: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:38:39: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Fri, 10 Dec 2021 21:38:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:38:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:38:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.10_summits.bed INFO @ Fri, 10 Dec 2021 21:38:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2970 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:39:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:39:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:39:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:39:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978872/ERX3978872.20_summits.bed INFO @ Fri, 10 Dec 2021 21:39:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1226 records, 4 fields): 3 millis CompletedMACS2peakCalling