Job ID = 16439410 SRX = SRX11245074 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:05:05 prefetch.2.10.7: 1) Downloading 'SRR14932339'... 2022-08-02T06:05:06 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:05:51 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:05:51 prefetch.2.10.7: 1) 'SRR14932339' was downloaded successfully 2022-08-02T06:05:51 prefetch.2.10.7: 'SRR14932339' has 0 unresolved dependencies Read 22908245 spots for SRR14932339/SRR14932339.sra Written 22908245 spots for SRR14932339/SRR14932339.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440020 ("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: 01:26:18 22908245 reads; of these: 22908245 (100.00%) were paired; of these: 6975604 (30.45%) aligned concordantly 0 times 11046128 (48.22%) aligned concordantly exactly 1 time 4886513 (21.33%) aligned concordantly >1 times ---- 6975604 pairs aligned concordantly 0 times; of these: 2215402 (31.76%) aligned discordantly 1 time ---- 4760202 pairs aligned 0 times concordantly or discordantly; of these: 9520404 mates make up the pairs; of these: 7263053 (76.29%) aligned 0 times 555836 (5.84%) aligned exactly 1 time 1701515 (17.87%) aligned >1 times 84.15% overall alignment rate Time searching: 01:26:18 Overall time: 01:26:18 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] 4573341 / 18008318 = 0.2540 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.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 @ Tue, 02 Aug 2022 16:47:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:47:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:47:16: 1000000 INFO @ Tue, 02 Aug 2022 16:47:24: 2000000 INFO @ Tue, 02 Aug 2022 16:47:33: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:47:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.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 @ Tue, 02 Aug 2022 16:47:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:47:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:47:41: 4000000 INFO @ Tue, 02 Aug 2022 16:47:45: 1000000 INFO @ Tue, 02 Aug 2022 16:47:50: 5000000 INFO @ Tue, 02 Aug 2022 16:47:53: 2000000 INFO @ Tue, 02 Aug 2022 16:47:59: 6000000 INFO @ Tue, 02 Aug 2022 16:48:02: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:48:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.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 @ Tue, 02 Aug 2022 16:48:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:48:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:48:08: 7000000 INFO @ Tue, 02 Aug 2022 16:48:10: 4000000 INFO @ Tue, 02 Aug 2022 16:48:16: 1000000 INFO @ Tue, 02 Aug 2022 16:48:17: 8000000 INFO @ Tue, 02 Aug 2022 16:48:18: 5000000 INFO @ Tue, 02 Aug 2022 16:48:24: 2000000 INFO @ Tue, 02 Aug 2022 16:48:26: 9000000 INFO @ Tue, 02 Aug 2022 16:48:26: 6000000 INFO @ Tue, 02 Aug 2022 16:48:33: 3000000 INFO @ Tue, 02 Aug 2022 16:48:35: 7000000 INFO @ Tue, 02 Aug 2022 16:48:35: 10000000 INFO @ Tue, 02 Aug 2022 16:48:41: 4000000 INFO @ Tue, 02 Aug 2022 16:48:43: 8000000 INFO @ Tue, 02 Aug 2022 16:48:44: 11000000 INFO @ Tue, 02 Aug 2022 16:48:50: 5000000 INFO @ Tue, 02 Aug 2022 16:48:51: 9000000 INFO @ Tue, 02 Aug 2022 16:48:53: 12000000 INFO @ Tue, 02 Aug 2022 16:48:58: 6000000 INFO @ Tue, 02 Aug 2022 16:49:00: 10000000 INFO @ Tue, 02 Aug 2022 16:49:02: 13000000 INFO @ Tue, 02 Aug 2022 16:49:06: 7000000 INFO @ Tue, 02 Aug 2022 16:49:08: 11000000 INFO @ Tue, 02 Aug 2022 16:49:11: 14000000 INFO @ Tue, 02 Aug 2022 16:49:15: 8000000 INFO @ Tue, 02 Aug 2022 16:49:17: 12000000 INFO @ Tue, 02 Aug 2022 16:49:20: 15000000 INFO @ Tue, 02 Aug 2022 16:49:23: 9000000 INFO @ Tue, 02 Aug 2022 16:49:25: 13000000 INFO @ Tue, 02 Aug 2022 16:49:29: 16000000 INFO @ Tue, 02 Aug 2022 16:49:32: 10000000 INFO @ Tue, 02 Aug 2022 16:49:33: 14000000 INFO @ Tue, 02 Aug 2022 16:49:38: 17000000 INFO @ Tue, 02 Aug 2022 16:49:40: 11000000 INFO @ Tue, 02 Aug 2022 16:49:42: 15000000 INFO @ Tue, 02 Aug 2022 16:49:46: 18000000 INFO @ Tue, 02 Aug 2022 16:49:49: 12000000 INFO @ Tue, 02 Aug 2022 16:49:50: 16000000 INFO @ Tue, 02 Aug 2022 16:49:55: 19000000 INFO @ Tue, 02 Aug 2022 16:49:57: 13000000 INFO @ Tue, 02 Aug 2022 16:49:58: 17000000 INFO @ Tue, 02 Aug 2022 16:50:04: 20000000 INFO @ Tue, 02 Aug 2022 16:50:05: 14000000 INFO @ Tue, 02 Aug 2022 16:50:06: 18000000 INFO @ Tue, 02 Aug 2022 16:50:13: 21000000 INFO @ Tue, 02 Aug 2022 16:50:13: 15000000 INFO @ Tue, 02 Aug 2022 16:50:14: 19000000 INFO @ Tue, 02 Aug 2022 16:50:22: 16000000 INFO @ Tue, 02 Aug 2022 16:50:22: 22000000 INFO @ Tue, 02 Aug 2022 16:50:23: 20000000 INFO @ Tue, 02 Aug 2022 16:50:30: 17000000 INFO @ Tue, 02 Aug 2022 16:50:31: 23000000 INFO @ Tue, 02 Aug 2022 16:50:31: 21000000 INFO @ Tue, 02 Aug 2022 16:50:38: 18000000 INFO @ Tue, 02 Aug 2022 16:50:39: 22000000 INFO @ Tue, 02 Aug 2022 16:50:39: 24000000 INFO @ Tue, 02 Aug 2022 16:50:46: 19000000 INFO @ Tue, 02 Aug 2022 16:50:47: 23000000 INFO @ Tue, 02 Aug 2022 16:50:48: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:50:54: 20000000 INFO @ Tue, 02 Aug 2022 16:50:56: 24000000 INFO @ Tue, 02 Aug 2022 16:50:58: 26000000 INFO @ Tue, 02 Aug 2022 16:51:02: 21000000 INFO @ Tue, 02 Aug 2022 16:51:04: 25000000 INFO @ Tue, 02 Aug 2022 16:51:07: 27000000 INFO @ Tue, 02 Aug 2022 16:51:11: 22000000 INFO @ Tue, 02 Aug 2022 16:51:12: 26000000 INFO @ Tue, 02 Aug 2022 16:51:15: 28000000 INFO @ Tue, 02 Aug 2022 16:51:19: 23000000 INFO @ Tue, 02 Aug 2022 16:51:20: 27000000 INFO @ Tue, 02 Aug 2022 16:51:24: 29000000 INFO @ Tue, 02 Aug 2022 16:51:27: 24000000 INFO @ Tue, 02 Aug 2022 16:51:28: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:51:28: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:51:28: #1 total tags in treatment: 11888528 INFO @ Tue, 02 Aug 2022 16:51:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:51:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:51:28: 28000000 INFO @ Tue, 02 Aug 2022 16:51:28: #1 tags after filtering in treatment: 11165240 INFO @ Tue, 02 Aug 2022 16:51:28: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 16:51:28: #1 finished! INFO @ Tue, 02 Aug 2022 16:51:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:51:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:51:29: #2 number of paired peaks: 242 WARNING @ Tue, 02 Aug 2022 16:51:29: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 02 Aug 2022 16:51:29: start model_add_line... INFO @ Tue, 02 Aug 2022 16:51:29: start X-correlation... INFO @ Tue, 02 Aug 2022 16:51:29: end of X-cor INFO @ Tue, 02 Aug 2022 16:51:29: #2 finished! INFO @ Tue, 02 Aug 2022 16:51:29: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 16:51:29: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 02 Aug 2022 16:51:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.05_model.r WARNING @ Tue, 02 Aug 2022 16:51:29: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:51:29: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Tue, 02 Aug 2022 16:51:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:51:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:51:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:51:35: 25000000 INFO @ Tue, 02 Aug 2022 16:51:36: 29000000 INFO @ Tue, 02 Aug 2022 16:51:39: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:51:39: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:51:39: #1 total tags in treatment: 11888528 INFO @ Tue, 02 Aug 2022 16:51:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:51:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:51:39: #1 tags after filtering in treatment: 11165240 INFO @ Tue, 02 Aug 2022 16:51:39: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 16:51:39: #1 finished! INFO @ Tue, 02 Aug 2022 16:51:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:51:40: #2 number of paired peaks: 242 WARNING @ Tue, 02 Aug 2022 16:51:40: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 02 Aug 2022 16:51:40: start model_add_line... INFO @ Tue, 02 Aug 2022 16:51:40: start X-correlation... INFO @ Tue, 02 Aug 2022 16:51:40: end of X-cor INFO @ Tue, 02 Aug 2022 16:51:40: #2 finished! INFO @ Tue, 02 Aug 2022 16:51:40: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 16:51:40: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 02 Aug 2022 16:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.10_model.r WARNING @ Tue, 02 Aug 2022 16:51:40: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:51:40: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Tue, 02 Aug 2022 16:51:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:51:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:51:43: 26000000 INFO @ Tue, 02 Aug 2022 16:51:51: 27000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:51:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:51:58: 28000000 INFO @ Tue, 02 Aug 2022 16:52:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:52:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:52:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.05_summits.bed INFO @ Tue, 02 Aug 2022 16:52:05: Done! INFO @ Tue, 02 Aug 2022 16:52:05: 29000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4493 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:52:07: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:52:07: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:52:07: #1 total tags in treatment: 11888528 INFO @ Tue, 02 Aug 2022 16:52:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:52:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:52:08: #1 tags after filtering in treatment: 11165240 INFO @ Tue, 02 Aug 2022 16:52:08: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 16:52:08: #1 finished! INFO @ Tue, 02 Aug 2022 16:52:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:52:08: #2 number of paired peaks: 242 WARNING @ Tue, 02 Aug 2022 16:52:08: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 02 Aug 2022 16:52:08: start model_add_line... INFO @ Tue, 02 Aug 2022 16:52:08: start X-correlation... INFO @ Tue, 02 Aug 2022 16:52:09: end of X-cor INFO @ Tue, 02 Aug 2022 16:52:09: #2 finished! INFO @ Tue, 02 Aug 2022 16:52:09: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 16:52:09: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 02 Aug 2022 16:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.20_model.r WARNING @ Tue, 02 Aug 2022 16:52:09: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:52:09: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Tue, 02 Aug 2022 16:52:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:52:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:52:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:52:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:52:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.10_summits.bed INFO @ Tue, 02 Aug 2022 16:52:15: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2215 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:52:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:52:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:52:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:52:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245074/SRX11245074.20_summits.bed INFO @ Tue, 02 Aug 2022 16:52:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (924 records, 4 fields): 39 millis CompletedMACS2peakCalling