Job ID = 14168805 SRX = ERX3978775 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12633211 spots for ERR3975796/ERR3975796.sra Written 12633211 spots for ERR3975796/ERR3975796.sra Read 17653140 spots for ERR3975807/ERR3975807.sra Written 17653140 spots for ERR3975807/ERR3975807.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169910 ("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: 00:52:29 30286351 reads; of these: 30286351 (100.00%) were paired; of these: 11455349 (37.82%) aligned concordantly 0 times 5844220 (19.30%) aligned concordantly exactly 1 time 12986782 (42.88%) aligned concordantly >1 times ---- 11455349 pairs aligned concordantly 0 times; of these: 1708312 (14.91%) aligned discordantly 1 time ---- 9747037 pairs aligned 0 times concordantly or discordantly; of these: 19494074 mates make up the pairs; of these: 10264655 (52.66%) aligned 0 times 448924 (2.30%) aligned exactly 1 time 8780495 (45.04%) aligned >1 times 83.05% overall alignment rate Time searching: 00:52:29 Overall time: 00:52:29 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 36 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] 11314393 / 20349947 = 0.5560 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 21:35:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.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 21:35:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:35:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:35:39: 1000000 INFO @ Fri, 10 Dec 2021 21:35:46: 2000000 INFO @ Fri, 10 Dec 2021 21:35:53: 3000000 INFO @ Fri, 10 Dec 2021 21:36:00: 4000000 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 21:36:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.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 21:36:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:36:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:36:07: 5000000 INFO @ Fri, 10 Dec 2021 21:36:10: 1000000 INFO @ Fri, 10 Dec 2021 21:36:15: 6000000 INFO @ Fri, 10 Dec 2021 21:36:18: 2000000 INFO @ Fri, 10 Dec 2021 21:36:23: 7000000 INFO @ Fri, 10 Dec 2021 21:36:26: 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 21:36:31: 8000000 INFO @ Fri, 10 Dec 2021 21:36:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.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 21:36:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:36:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:36:34: 4000000 INFO @ Fri, 10 Dec 2021 21:36:39: 9000000 INFO @ Fri, 10 Dec 2021 21:36:41: 1000000 INFO @ Fri, 10 Dec 2021 21:36:43: 5000000 INFO @ Fri, 10 Dec 2021 21:36:48: 10000000 INFO @ Fri, 10 Dec 2021 21:36:50: 2000000 INFO @ Fri, 10 Dec 2021 21:36:52: 6000000 INFO @ Fri, 10 Dec 2021 21:36:57: 11000000 INFO @ Fri, 10 Dec 2021 21:36:59: 3000000 INFO @ Fri, 10 Dec 2021 21:37:00: 7000000 INFO @ Fri, 10 Dec 2021 21:37:05: 12000000 INFO @ Fri, 10 Dec 2021 21:37:07: 4000000 INFO @ Fri, 10 Dec 2021 21:37:09: 8000000 INFO @ Fri, 10 Dec 2021 21:37:13: 13000000 INFO @ Fri, 10 Dec 2021 21:37:16: 5000000 INFO @ Fri, 10 Dec 2021 21:37:18: 9000000 INFO @ Fri, 10 Dec 2021 21:37:21: 14000000 INFO @ Fri, 10 Dec 2021 21:37:24: 6000000 INFO @ Fri, 10 Dec 2021 21:37:26: 10000000 INFO @ Fri, 10 Dec 2021 21:37:29: 15000000 INFO @ Fri, 10 Dec 2021 21:37:32: 7000000 INFO @ Fri, 10 Dec 2021 21:37:34: 11000000 INFO @ Fri, 10 Dec 2021 21:37:36: 16000000 INFO @ Fri, 10 Dec 2021 21:37:41: 8000000 INFO @ Fri, 10 Dec 2021 21:37:43: 12000000 INFO @ Fri, 10 Dec 2021 21:37:44: 17000000 INFO @ Fri, 10 Dec 2021 21:37:49: 9000000 INFO @ Fri, 10 Dec 2021 21:37:50: 13000000 INFO @ Fri, 10 Dec 2021 21:37:52: 18000000 INFO @ Fri, 10 Dec 2021 21:37:57: 10000000 INFO @ Fri, 10 Dec 2021 21:37:58: 14000000 INFO @ Fri, 10 Dec 2021 21:38:00: 19000000 INFO @ Fri, 10 Dec 2021 21:38:05: 11000000 INFO @ Fri, 10 Dec 2021 21:38:06: 15000000 INFO @ Fri, 10 Dec 2021 21:38:07: 20000000 INFO @ Fri, 10 Dec 2021 21:38:13: 12000000 INFO @ Fri, 10 Dec 2021 21:38:14: 16000000 INFO @ Fri, 10 Dec 2021 21:38:15: 21000000 INFO @ Fri, 10 Dec 2021 21:38:21: 13000000 INFO @ Fri, 10 Dec 2021 21:38:21: 17000000 INFO @ Fri, 10 Dec 2021 21:38:23: 22000000 INFO @ Fri, 10 Dec 2021 21:38:29: 14000000 INFO @ Fri, 10 Dec 2021 21:38:29: 18000000 INFO @ Fri, 10 Dec 2021 21:38:30: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:38:36: 15000000 INFO @ Fri, 10 Dec 2021 21:38:37: 19000000 INFO @ Fri, 10 Dec 2021 21:38:38: 24000000 INFO @ Fri, 10 Dec 2021 21:38:44: 16000000 INFO @ Fri, 10 Dec 2021 21:38:44: 20000000 INFO @ Fri, 10 Dec 2021 21:38:46: 25000000 INFO @ Fri, 10 Dec 2021 21:38:52: 17000000 INFO @ Fri, 10 Dec 2021 21:38:52: 21000000 INFO @ Fri, 10 Dec 2021 21:38:54: 26000000 INFO @ Fri, 10 Dec 2021 21:38:59: 18000000 INFO @ Fri, 10 Dec 2021 21:38:59: 22000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:39:02: 27000000 INFO @ Fri, 10 Dec 2021 21:39:07: 19000000 INFO @ Fri, 10 Dec 2021 21:39:07: 23000000 INFO @ Fri, 10 Dec 2021 21:39:07: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:39:07: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:39:07: #1 total tags in treatment: 7717403 INFO @ Fri, 10 Dec 2021 21:39:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:39:07: #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 21:39:07: #1 tags after filtering in treatment: 5446880 INFO @ Fri, 10 Dec 2021 21:39:07: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 21:39:07: #1 finished! INFO @ Fri, 10 Dec 2021 21:39:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:39:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:39:08: #2 number of paired peaks: 3301 INFO @ Fri, 10 Dec 2021 21:39:08: start model_add_line... INFO @ Fri, 10 Dec 2021 21:39:08: start X-correlation... INFO @ Fri, 10 Dec 2021 21:39:08: end of X-cor INFO @ Fri, 10 Dec 2021 21:39:08: #2 finished! INFO @ Fri, 10 Dec 2021 21:39:08: #2 predicted fragment length is 193 bps INFO @ Fri, 10 Dec 2021 21:39:08: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 10 Dec 2021 21:39:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.05_model.r WARNING @ Fri, 10 Dec 2021 21:39:08: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:39:08: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Fri, 10 Dec 2021 21:39:08: #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 21:39:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:39:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:39:14: 20000000 INFO @ Fri, 10 Dec 2021 21:39:15: 24000000 INFO @ Fri, 10 Dec 2021 21:39:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:39:22: 21000000 INFO @ Fri, 10 Dec 2021 21:39:22: 25000000 INFO @ Fri, 10 Dec 2021 21:39:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:39:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:39:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.05_summits.bed INFO @ Fri, 10 Dec 2021 21:39:26: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8765 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:39:29: 22000000 INFO @ Fri, 10 Dec 2021 21:39:30: 26000000 INFO @ Fri, 10 Dec 2021 21:39:36: 23000000 INFO @ Fri, 10 Dec 2021 21:39:38: 27000000 INFO @ Fri, 10 Dec 2021 21:39:44: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:39:44: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:39:44: #1 total tags in treatment: 7717403 INFO @ Fri, 10 Dec 2021 21:39:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:39:44: #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 21:39:44: #1 tags after filtering in treatment: 5446880 INFO @ Fri, 10 Dec 2021 21:39:44: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 21:39:44: #1 finished! INFO @ Fri, 10 Dec 2021 21:39:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:39:44: 24000000 INFO @ Fri, 10 Dec 2021 21:39:44: #2 number of paired peaks: 3301 INFO @ Fri, 10 Dec 2021 21:39:44: start model_add_line... INFO @ Fri, 10 Dec 2021 21:39:44: start X-correlation... INFO @ Fri, 10 Dec 2021 21:39:44: end of X-cor INFO @ Fri, 10 Dec 2021 21:39:44: #2 finished! INFO @ Fri, 10 Dec 2021 21:39:44: #2 predicted fragment length is 193 bps INFO @ Fri, 10 Dec 2021 21:39:44: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 10 Dec 2021 21:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.10_model.r WARNING @ Fri, 10 Dec 2021 21:39:44: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:39:44: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Fri, 10 Dec 2021 21:39:44: #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 21:39:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:39:51: 25000000 INFO @ Fri, 10 Dec 2021 21:39:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:39:59: 26000000 INFO @ Fri, 10 Dec 2021 21:40:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:40:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:40:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.10_summits.bed INFO @ Fri, 10 Dec 2021 21:40:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4978 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:40:06: 27000000 INFO @ Fri, 10 Dec 2021 21:40:10: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:40:10: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:40:10: #1 total tags in treatment: 7717403 INFO @ Fri, 10 Dec 2021 21:40:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:40:10: #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 21:40:11: #1 tags after filtering in treatment: 5446880 INFO @ Fri, 10 Dec 2021 21:40:11: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 21:40:11: #1 finished! INFO @ Fri, 10 Dec 2021 21:40:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:40:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:40:11: #2 number of paired peaks: 3301 INFO @ Fri, 10 Dec 2021 21:40:11: start model_add_line... INFO @ Fri, 10 Dec 2021 21:40:11: start X-correlation... INFO @ Fri, 10 Dec 2021 21:40:11: end of X-cor INFO @ Fri, 10 Dec 2021 21:40:11: #2 finished! INFO @ Fri, 10 Dec 2021 21:40:11: #2 predicted fragment length is 193 bps INFO @ Fri, 10 Dec 2021 21:40:11: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 10 Dec 2021 21:40:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.20_model.r WARNING @ Fri, 10 Dec 2021 21:40:11: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:40:11: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Fri, 10 Dec 2021 21:40:11: #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 21:40:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:40:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:40:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:40:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:40:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:40:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978775/ERX3978775.20_summits.bed INFO @ Fri, 10 Dec 2021 21:40:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1711 records, 4 fields): 3 millis CompletedMACS2peakCalling