Job ID = 16435528 SRX = SRX13336907 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:43:24 25559692 reads; of these: 25559692 (100.00%) were paired; of these: 11186033 (43.76%) aligned concordantly 0 times 12263347 (47.98%) aligned concordantly exactly 1 time 2110312 (8.26%) aligned concordantly >1 times ---- 11186033 pairs aligned concordantly 0 times; of these: 4288479 (38.34%) aligned discordantly 1 time ---- 6897554 pairs aligned 0 times concordantly or discordantly; of these: 13795108 mates make up the pairs; of these: 12233945 (88.68%) aligned 0 times 715845 (5.19%) aligned exactly 1 time 845318 (6.13%) aligned >1 times 76.07% overall alignment rate Time searching: 00:43:24 Overall time: 00:43:24 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 32 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 2631642 / 18580826 = 0.1416 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 11:46:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.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 @ Tue, 02 Aug 2022 11:46:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:46:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:46:54: 1000000 INFO @ Tue, 02 Aug 2022 11:47:04: 2000000 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 11:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.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 @ Tue, 02 Aug 2022 11:47:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:47:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:47:14: 3000000 INFO @ Tue, 02 Aug 2022 11:47:24: 1000000 INFO @ Tue, 02 Aug 2022 11:47:25: 4000000 INFO @ Tue, 02 Aug 2022 11:47:34: 2000000 INFO @ Tue, 02 Aug 2022 11:47:36: 5000000 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 11:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.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 @ Tue, 02 Aug 2022 11:47:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:47:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:47:44: 3000000 INFO @ Tue, 02 Aug 2022 11:47:47: 6000000 INFO @ Tue, 02 Aug 2022 11:47:54: 1000000 INFO @ Tue, 02 Aug 2022 11:47:55: 4000000 INFO @ Tue, 02 Aug 2022 11:47:57: 7000000 INFO @ Tue, 02 Aug 2022 11:48:05: 2000000 INFO @ Tue, 02 Aug 2022 11:48:05: 5000000 INFO @ Tue, 02 Aug 2022 11:48:08: 8000000 INFO @ Tue, 02 Aug 2022 11:48:15: 3000000 INFO @ Tue, 02 Aug 2022 11:48:15: 6000000 INFO @ Tue, 02 Aug 2022 11:48:19: 9000000 INFO @ Tue, 02 Aug 2022 11:48:25: 4000000 INFO @ Tue, 02 Aug 2022 11:48:26: 7000000 INFO @ Tue, 02 Aug 2022 11:48:30: 10000000 INFO @ Tue, 02 Aug 2022 11:48:35: 5000000 INFO @ Tue, 02 Aug 2022 11:48:36: 8000000 INFO @ Tue, 02 Aug 2022 11:48:39: 11000000 INFO @ Tue, 02 Aug 2022 11:48:45: 6000000 INFO @ Tue, 02 Aug 2022 11:48:47: 9000000 INFO @ Tue, 02 Aug 2022 11:48:49: 12000000 INFO @ Tue, 02 Aug 2022 11:48:55: 7000000 INFO @ Tue, 02 Aug 2022 11:48:58: 10000000 INFO @ Tue, 02 Aug 2022 11:48:59: 13000000 INFO @ Tue, 02 Aug 2022 11:49:05: 8000000 INFO @ Tue, 02 Aug 2022 11:49:08: 11000000 INFO @ Tue, 02 Aug 2022 11:49:08: 14000000 INFO @ Tue, 02 Aug 2022 11:49:15: 9000000 INFO @ Tue, 02 Aug 2022 11:49:18: 15000000 INFO @ Tue, 02 Aug 2022 11:49:19: 12000000 INFO @ Tue, 02 Aug 2022 11:49:25: 10000000 INFO @ Tue, 02 Aug 2022 11:49:28: 16000000 INFO @ Tue, 02 Aug 2022 11:49:30: 13000000 INFO @ Tue, 02 Aug 2022 11:49:35: 11000000 INFO @ Tue, 02 Aug 2022 11:49:38: 17000000 INFO @ Tue, 02 Aug 2022 11:49:40: 14000000 INFO @ Tue, 02 Aug 2022 11:49:45: 12000000 INFO @ Tue, 02 Aug 2022 11:49:48: 18000000 INFO @ Tue, 02 Aug 2022 11:49:51: 15000000 INFO @ Tue, 02 Aug 2022 11:49:55: 13000000 INFO @ Tue, 02 Aug 2022 11:49:57: 19000000 INFO @ Tue, 02 Aug 2022 11:50:02: 16000000 INFO @ Tue, 02 Aug 2022 11:50:05: 14000000 INFO @ Tue, 02 Aug 2022 11:50:07: 20000000 INFO @ Tue, 02 Aug 2022 11:50:12: 17000000 INFO @ Tue, 02 Aug 2022 11:50:15: 15000000 INFO @ Tue, 02 Aug 2022 11:50:17: 21000000 INFO @ Tue, 02 Aug 2022 11:50:23: 18000000 INFO @ Tue, 02 Aug 2022 11:50:24: 16000000 INFO @ Tue, 02 Aug 2022 11:50:27: 22000000 INFO @ Tue, 02 Aug 2022 11:50:34: 19000000 INFO @ Tue, 02 Aug 2022 11:50:34: 17000000 INFO @ Tue, 02 Aug 2022 11:50:37: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:50:44: 18000000 INFO @ Tue, 02 Aug 2022 11:50:44: 20000000 INFO @ Tue, 02 Aug 2022 11:50:46: 24000000 INFO @ Tue, 02 Aug 2022 11:50:54: 19000000 INFO @ Tue, 02 Aug 2022 11:50:55: 21000000 INFO @ Tue, 02 Aug 2022 11:50:56: 25000000 INFO @ Tue, 02 Aug 2022 11:51:04: 20000000 INFO @ Tue, 02 Aug 2022 11:51:06: 22000000 INFO @ Tue, 02 Aug 2022 11:51:06: 26000000 INFO @ Tue, 02 Aug 2022 11:51:14: 21000000 INFO @ Tue, 02 Aug 2022 11:51:16: 23000000 INFO @ Tue, 02 Aug 2022 11:51:16: 27000000 INFO @ Tue, 02 Aug 2022 11:51:24: 22000000 INFO @ Tue, 02 Aug 2022 11:51:26: 28000000 INFO @ Tue, 02 Aug 2022 11:51:26: 24000000 INFO @ Tue, 02 Aug 2022 11:51:34: 23000000 INFO @ Tue, 02 Aug 2022 11:51:36: 29000000 INFO @ Tue, 02 Aug 2022 11:51:37: 25000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:51:43: 24000000 INFO @ Tue, 02 Aug 2022 11:51:45: 30000000 INFO @ Tue, 02 Aug 2022 11:51:47: 26000000 INFO @ Tue, 02 Aug 2022 11:51:53: 25000000 INFO @ Tue, 02 Aug 2022 11:51:55: 31000000 INFO @ Tue, 02 Aug 2022 11:51:58: 27000000 INFO @ Tue, 02 Aug 2022 11:52:03: 26000000 INFO @ Tue, 02 Aug 2022 11:52:05: 32000000 INFO @ Tue, 02 Aug 2022 11:52:09: 28000000 INFO @ Tue, 02 Aug 2022 11:52:13: 27000000 INFO @ Tue, 02 Aug 2022 11:52:15: 33000000 INFO @ Tue, 02 Aug 2022 11:52:19: 29000000 INFO @ Tue, 02 Aug 2022 11:52:22: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:52:22: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:52:22: #1 total tags in treatment: 12231421 INFO @ Tue, 02 Aug 2022 11:52:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:52:22: #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 11:52:22: #1 tags after filtering in treatment: 11229468 INFO @ Tue, 02 Aug 2022 11:52:22: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:52:22: #1 finished! INFO @ Tue, 02 Aug 2022 11:52:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:52:23: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 11:52:23: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 11:52:23: start model_add_line... INFO @ Tue, 02 Aug 2022 11:52:23: start X-correlation... INFO @ Tue, 02 Aug 2022 11:52:23: end of X-cor INFO @ Tue, 02 Aug 2022 11:52:23: #2 finished! INFO @ Tue, 02 Aug 2022 11:52:23: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 11:52:23: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 11:52:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.05_model.r WARNING @ Tue, 02 Aug 2022 11:52:23: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:52:23: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Tue, 02 Aug 2022 11:52:23: #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 11:52:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:52:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:52:23: 28000000 INFO @ Tue, 02 Aug 2022 11:52:29: 30000000 INFO @ Tue, 02 Aug 2022 11:52:33: 29000000 INFO @ Tue, 02 Aug 2022 11:52:39: 31000000 INFO @ Tue, 02 Aug 2022 11:52:43: 30000000 INFO @ Tue, 02 Aug 2022 11:52:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:52:50: 32000000 INFO @ Tue, 02 Aug 2022 11:52:52: 31000000 INFO @ Tue, 02 Aug 2022 11:52:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:52:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:52:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.05_summits.bed INFO @ Tue, 02 Aug 2022 11:52:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (482 records, 4 fields): 269 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:53:00: 33000000 INFO @ Tue, 02 Aug 2022 11:53:02: 32000000 INFO @ Tue, 02 Aug 2022 11:53:06: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:53:06: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:53:06: #1 total tags in treatment: 12231421 INFO @ Tue, 02 Aug 2022 11:53:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:53:06: #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 11:53:06: #1 tags after filtering in treatment: 11229468 INFO @ Tue, 02 Aug 2022 11:53:06: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:53:06: #1 finished! INFO @ Tue, 02 Aug 2022 11:53:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:53:07: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 11:53:07: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 11:53:07: start model_add_line... INFO @ Tue, 02 Aug 2022 11:53:07: start X-correlation... INFO @ Tue, 02 Aug 2022 11:53:07: end of X-cor INFO @ Tue, 02 Aug 2022 11:53:07: #2 finished! INFO @ Tue, 02 Aug 2022 11:53:07: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 11:53:07: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 11:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.10_model.r WARNING @ Tue, 02 Aug 2022 11:53:07: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:53:07: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Tue, 02 Aug 2022 11:53:07: #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 11:53:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:53:11: 33000000 INFO @ Tue, 02 Aug 2022 11:53:17: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:53:17: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:53:17: #1 total tags in treatment: 12231421 INFO @ Tue, 02 Aug 2022 11:53:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:53:17: #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 11:53:17: #1 tags after filtering in treatment: 11229468 INFO @ Tue, 02 Aug 2022 11:53:17: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:53:17: #1 finished! INFO @ Tue, 02 Aug 2022 11:53:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:53:18: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 11:53:18: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 11:53:18: start model_add_line... INFO @ Tue, 02 Aug 2022 11:53:18: start X-correlation... INFO @ Tue, 02 Aug 2022 11:53:18: end of X-cor INFO @ Tue, 02 Aug 2022 11:53:18: #2 finished! INFO @ Tue, 02 Aug 2022 11:53:18: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 11:53:18: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 11:53:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.20_model.r WARNING @ Tue, 02 Aug 2022 11:53:18: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:53:18: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Tue, 02 Aug 2022 11:53:18: #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 11:53:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:53:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:53:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:53:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.10_summits.bed INFO @ Tue, 02 Aug 2022 11:53:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (387 records, 4 fields): 193 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:53:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:53:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:53:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:53:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336907/SRX13336907.20_summits.bed INFO @ Tue, 02 Aug 2022 11:53:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (270 records, 4 fields): 19 millis CompletedMACS2peakCalling