Job ID = 14168328 SRX = ERX3978738 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24494729 spots for ERR3975747/ERR3975747.sra Written 24494729 spots for ERR3975747/ERR3975747.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169558 ("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: 00:51:58 24494729 reads; of these: 24494729 (100.00%) were paired; of these: 9498317 (38.78%) aligned concordantly 0 times 7984453 (32.60%) aligned concordantly exactly 1 time 7011959 (28.63%) aligned concordantly >1 times ---- 9498317 pairs aligned concordantly 0 times; of these: 2695636 (28.38%) aligned discordantly 1 time ---- 6802681 pairs aligned 0 times concordantly or discordantly; of these: 13605362 mates make up the pairs; of these: 8957075 (65.83%) aligned 0 times 461920 (3.40%) aligned exactly 1 time 4186367 (30.77%) aligned >1 times 81.72% overall alignment rate Time searching: 00:51:58 Overall time: 00:51:58 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 28 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] 5498188 / 17581029 = 0.3127 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 18:31:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.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 18:31:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:31:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:31:48: 1000000 INFO @ Fri, 10 Dec 2021 18:31:56: 2000000 INFO @ Fri, 10 Dec 2021 18:32:03: 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 @ Fri, 10 Dec 2021 18:32:10: 4000000 INFO @ Fri, 10 Dec 2021 18:32:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.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 18:32:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:32:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:32:19: 5000000 INFO @ Fri, 10 Dec 2021 18:32:20: 1000000 INFO @ Fri, 10 Dec 2021 18:32:28: 6000000 INFO @ Fri, 10 Dec 2021 18:32:29: 2000000 INFO @ Fri, 10 Dec 2021 18:32:36: 7000000 INFO @ Fri, 10 Dec 2021 18:32:38: 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 @ Fri, 10 Dec 2021 18:32:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.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 18:32:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:32:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:32:45: 8000000 INFO @ Fri, 10 Dec 2021 18:32:47: 4000000 INFO @ Fri, 10 Dec 2021 18:32:50: 1000000 INFO @ Fri, 10 Dec 2021 18:32:54: 9000000 INFO @ Fri, 10 Dec 2021 18:32:56: 5000000 INFO @ Fri, 10 Dec 2021 18:32:59: 2000000 INFO @ Fri, 10 Dec 2021 18:33:03: 10000000 INFO @ Fri, 10 Dec 2021 18:33:05: 6000000 INFO @ Fri, 10 Dec 2021 18:33:08: 3000000 INFO @ Fri, 10 Dec 2021 18:33:12: 11000000 INFO @ Fri, 10 Dec 2021 18:33:14: 7000000 INFO @ Fri, 10 Dec 2021 18:33:17: 4000000 INFO @ Fri, 10 Dec 2021 18:33:21: 12000000 INFO @ Fri, 10 Dec 2021 18:33:23: 8000000 INFO @ Fri, 10 Dec 2021 18:33:26: 5000000 INFO @ Fri, 10 Dec 2021 18:33:30: 13000000 INFO @ Fri, 10 Dec 2021 18:33:32: 9000000 INFO @ Fri, 10 Dec 2021 18:33:36: 6000000 INFO @ Fri, 10 Dec 2021 18:33:39: 14000000 INFO @ Fri, 10 Dec 2021 18:33:41: 10000000 INFO @ Fri, 10 Dec 2021 18:33:45: 7000000 INFO @ Fri, 10 Dec 2021 18:33:48: 15000000 INFO @ Fri, 10 Dec 2021 18:33:50: 11000000 INFO @ Fri, 10 Dec 2021 18:33:54: 8000000 INFO @ Fri, 10 Dec 2021 18:33:57: 16000000 INFO @ Fri, 10 Dec 2021 18:33:58: 12000000 INFO @ Fri, 10 Dec 2021 18:34:03: 9000000 INFO @ Fri, 10 Dec 2021 18:34:06: 17000000 INFO @ Fri, 10 Dec 2021 18:34:07: 13000000 INFO @ Fri, 10 Dec 2021 18:34:12: 10000000 INFO @ Fri, 10 Dec 2021 18:34:15: 18000000 INFO @ Fri, 10 Dec 2021 18:34:16: 14000000 INFO @ Fri, 10 Dec 2021 18:34:21: 11000000 INFO @ Fri, 10 Dec 2021 18:34:23: 19000000 INFO @ Fri, 10 Dec 2021 18:34:25: 15000000 INFO @ Fri, 10 Dec 2021 18:34:30: 12000000 INFO @ Fri, 10 Dec 2021 18:34:32: 20000000 INFO @ Fri, 10 Dec 2021 18:34:34: 16000000 INFO @ Fri, 10 Dec 2021 18:34:39: 13000000 INFO @ Fri, 10 Dec 2021 18:34:40: 21000000 INFO @ Fri, 10 Dec 2021 18:34:43: 17000000 INFO @ Fri, 10 Dec 2021 18:34:47: 14000000 INFO @ Fri, 10 Dec 2021 18:34:49: 22000000 INFO @ Fri, 10 Dec 2021 18:34:52: 18000000 INFO @ Fri, 10 Dec 2021 18:34:56: 15000000 INFO @ Fri, 10 Dec 2021 18:34:58: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:35:00: 19000000 INFO @ Fri, 10 Dec 2021 18:35:05: 16000000 INFO @ Fri, 10 Dec 2021 18:35:06: 24000000 INFO @ Fri, 10 Dec 2021 18:35:09: 20000000 INFO @ Fri, 10 Dec 2021 18:35:14: 17000000 INFO @ Fri, 10 Dec 2021 18:35:15: 25000000 INFO @ Fri, 10 Dec 2021 18:35:17: 21000000 INFO @ Fri, 10 Dec 2021 18:35:23: 18000000 INFO @ Fri, 10 Dec 2021 18:35:24: 26000000 INFO @ Fri, 10 Dec 2021 18:35:26: 22000000 INFO @ Fri, 10 Dec 2021 18:35:32: 19000000 INFO @ Fri, 10 Dec 2021 18:35:33: 27000000 INFO @ Fri, 10 Dec 2021 18:35:34: 23000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:35:40: 20000000 INFO @ Fri, 10 Dec 2021 18:35:42: 28000000 INFO @ Fri, 10 Dec 2021 18:35:43: 24000000 INFO @ Fri, 10 Dec 2021 18:35:49: 21000000 INFO @ Fri, 10 Dec 2021 18:35:51: 29000000 INFO @ Fri, 10 Dec 2021 18:35:51: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:35:51: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:35:51: #1 total tags in treatment: 9659224 INFO @ Fri, 10 Dec 2021 18:35:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:35:51: #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 18:35:52: #1 tags after filtering in treatment: 7025309 INFO @ Fri, 10 Dec 2021 18:35:52: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 18:35:52: #1 finished! INFO @ Fri, 10 Dec 2021 18:35:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:35:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:35:52: 25000000 INFO @ Fri, 10 Dec 2021 18:35:52: #2 number of paired peaks: 2994 INFO @ Fri, 10 Dec 2021 18:35:52: start model_add_line... INFO @ Fri, 10 Dec 2021 18:35:52: start X-correlation... INFO @ Fri, 10 Dec 2021 18:35:52: end of X-cor INFO @ Fri, 10 Dec 2021 18:35:52: #2 finished! INFO @ Fri, 10 Dec 2021 18:35:52: #2 predicted fragment length is 203 bps INFO @ Fri, 10 Dec 2021 18:35:52: #2 alternative fragment length(s) may be 203 bps INFO @ Fri, 10 Dec 2021 18:35:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.05_model.r WARNING @ Fri, 10 Dec 2021 18:35:52: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:35:52: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Fri, 10 Dec 2021 18:35:52: #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 18:35:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:35:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:35:58: 22000000 INFO @ Fri, 10 Dec 2021 18:36:01: 26000000 INFO @ Fri, 10 Dec 2021 18:36:06: 23000000 INFO @ Fri, 10 Dec 2021 18:36:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:36:10: 27000000 INFO @ Fri, 10 Dec 2021 18:36:15: 24000000 INFO @ Fri, 10 Dec 2021 18:36:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.05_summits.bed INFO @ Fri, 10 Dec 2021 18:36:18: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11522 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:36:19: 28000000 INFO @ Fri, 10 Dec 2021 18:36:24: 25000000 INFO @ Fri, 10 Dec 2021 18:36:28: 29000000 INFO @ Fri, 10 Dec 2021 18:36:28: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:36:28: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:36:28: #1 total tags in treatment: 9659224 INFO @ Fri, 10 Dec 2021 18:36:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:36:28: #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 18:36:28: #1 tags after filtering in treatment: 7025309 INFO @ Fri, 10 Dec 2021 18:36:28: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 18:36:28: #1 finished! INFO @ Fri, 10 Dec 2021 18:36:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:36:29: #2 number of paired peaks: 2994 INFO @ Fri, 10 Dec 2021 18:36:29: start model_add_line... INFO @ Fri, 10 Dec 2021 18:36:29: start X-correlation... INFO @ Fri, 10 Dec 2021 18:36:29: end of X-cor INFO @ Fri, 10 Dec 2021 18:36:29: #2 finished! INFO @ Fri, 10 Dec 2021 18:36:29: #2 predicted fragment length is 203 bps INFO @ Fri, 10 Dec 2021 18:36:29: #2 alternative fragment length(s) may be 203 bps INFO @ Fri, 10 Dec 2021 18:36:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.10_model.r WARNING @ Fri, 10 Dec 2021 18:36:29: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:36:29: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Fri, 10 Dec 2021 18:36:29: #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 18:36:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:36:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:36:33: 26000000 INFO @ Fri, 10 Dec 2021 18:36:40: 27000000 INFO @ Fri, 10 Dec 2021 18:36:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:36:47: 28000000 INFO @ Fri, 10 Dec 2021 18:36:55: 29000000 INFO @ Fri, 10 Dec 2021 18:36:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:36:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:36:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.10_summits.bed INFO @ Fri, 10 Dec 2021 18:36:55: Done! INFO @ Fri, 10 Dec 2021 18:36:55: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:36:55: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:36:55: #1 total tags in treatment: 9659224 INFO @ Fri, 10 Dec 2021 18:36:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:36:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7165 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:36:55: #1 tags after filtering in treatment: 7025309 INFO @ Fri, 10 Dec 2021 18:36:55: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 18:36:55: #1 finished! INFO @ Fri, 10 Dec 2021 18:36:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:36:56: #2 number of paired peaks: 2994 INFO @ Fri, 10 Dec 2021 18:36:56: start model_add_line... INFO @ Fri, 10 Dec 2021 18:36:56: start X-correlation... INFO @ Fri, 10 Dec 2021 18:36:56: end of X-cor INFO @ Fri, 10 Dec 2021 18:36:56: #2 finished! INFO @ Fri, 10 Dec 2021 18:36:56: #2 predicted fragment length is 203 bps INFO @ Fri, 10 Dec 2021 18:36:56: #2 alternative fragment length(s) may be 203 bps INFO @ Fri, 10 Dec 2021 18:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.20_model.r WARNING @ Fri, 10 Dec 2021 18:36:56: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:36:56: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Fri, 10 Dec 2021 18:36:56: #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 18:36:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:36:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:37:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978738/ERX3978738.20_summits.bed INFO @ Fri, 10 Dec 2021 18:37:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2698 records, 4 fields): 5 millis CompletedMACS2peakCalling