Job ID = 4288855 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:22:31 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:22:31 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:22:31 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:22:31 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:23:25 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:23:25 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:30:51 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 37,545,291 reads read : 75,090,582 reads written : 37,545,291 reads 0-length : 37,545,291 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:02 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:42:25 37545291 reads; of these: 37545291 (100.00%) were unpaired; of these: 870099 (2.32%) aligned 0 times 25096325 (66.84%) aligned exactly 1 time 11578867 (30.84%) aligned >1 times 97.68% overall alignment rate Time searching: 00:42:32 Overall time: 00:42:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 1335994 / 36675192 = 0.0364 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Dec 2019 13:26:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:26:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:26:26: 1000000 INFO @ Tue, 10 Dec 2019 13:26:33: 2000000 INFO @ Tue, 10 Dec 2019 13:26:41: 3000000 INFO @ Tue, 10 Dec 2019 13:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Dec 2019 13:26:48: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:26:48: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:26:48: 4000000 INFO @ Tue, 10 Dec 2019 13:26:56: 5000000 INFO @ Tue, 10 Dec 2019 13:26:59: 1000000 INFO @ Tue, 10 Dec 2019 13:27:04: 6000000 INFO @ Tue, 10 Dec 2019 13:27:11: 2000000 INFO @ Tue, 10 Dec 2019 13:27:11: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Dec 2019 13:27:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:27:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:27:19: 8000000 INFO @ Tue, 10 Dec 2019 13:27:22: 3000000 INFO @ Tue, 10 Dec 2019 13:27:27: 9000000 INFO @ Tue, 10 Dec 2019 13:27:29: 1000000 INFO @ Tue, 10 Dec 2019 13:27:34: 4000000 INFO @ Tue, 10 Dec 2019 13:27:35: 10000000 INFO @ Tue, 10 Dec 2019 13:27:41: 2000000 INFO @ Tue, 10 Dec 2019 13:27:42: 11000000 INFO @ Tue, 10 Dec 2019 13:27:47: 5000000 INFO @ Tue, 10 Dec 2019 13:27:50: 12000000 INFO @ Tue, 10 Dec 2019 13:27:52: 3000000 INFO @ Tue, 10 Dec 2019 13:27:58: 13000000 INFO @ Tue, 10 Dec 2019 13:27:59: 6000000 INFO @ Tue, 10 Dec 2019 13:28:03: 4000000 INFO @ Tue, 10 Dec 2019 13:28:05: 14000000 INFO @ Tue, 10 Dec 2019 13:28:11: 7000000 INFO @ Tue, 10 Dec 2019 13:28:13: 15000000 INFO @ Tue, 10 Dec 2019 13:28:14: 5000000 INFO @ Tue, 10 Dec 2019 13:28:21: 16000000 INFO @ Tue, 10 Dec 2019 13:28:23: 8000000 INFO @ Tue, 10 Dec 2019 13:28:25: 6000000 INFO @ Tue, 10 Dec 2019 13:28:28: 17000000 INFO @ Tue, 10 Dec 2019 13:28:36: 9000000 INFO @ Tue, 10 Dec 2019 13:28:36: 18000000 INFO @ Tue, 10 Dec 2019 13:28:37: 7000000 INFO @ Tue, 10 Dec 2019 13:28:45: 19000000 INFO @ Tue, 10 Dec 2019 13:28:48: 10000000 INFO @ Tue, 10 Dec 2019 13:28:48: 8000000 INFO @ Tue, 10 Dec 2019 13:28:53: 20000000 INFO @ Tue, 10 Dec 2019 13:29:00: 9000000 INFO @ Tue, 10 Dec 2019 13:29:00: 11000000 INFO @ Tue, 10 Dec 2019 13:29:01: 21000000 INFO @ Tue, 10 Dec 2019 13:29:10: 22000000 INFO @ Tue, 10 Dec 2019 13:29:11: 10000000 INFO @ Tue, 10 Dec 2019 13:29:12: 12000000 INFO @ Tue, 10 Dec 2019 13:29:17: 23000000 INFO @ Tue, 10 Dec 2019 13:29:23: 11000000 INFO @ Tue, 10 Dec 2019 13:29:24: 13000000 INFO @ Tue, 10 Dec 2019 13:29:25: 24000000 INFO @ Tue, 10 Dec 2019 13:29:33: 25000000 INFO @ Tue, 10 Dec 2019 13:29:33: 12000000 INFO @ Tue, 10 Dec 2019 13:29:35: 14000000 INFO @ Tue, 10 Dec 2019 13:29:41: 26000000 INFO @ Tue, 10 Dec 2019 13:29:44: 13000000 INFO @ Tue, 10 Dec 2019 13:29:46: 15000000 INFO @ Tue, 10 Dec 2019 13:29:48: 27000000 INFO @ Tue, 10 Dec 2019 13:29:55: 14000000 INFO @ Tue, 10 Dec 2019 13:29:56: 28000000 INFO @ Tue, 10 Dec 2019 13:29:58: 16000000 INFO @ Tue, 10 Dec 2019 13:30:04: 29000000 INFO @ Tue, 10 Dec 2019 13:30:05: 15000000 INFO @ Tue, 10 Dec 2019 13:30:09: 17000000 INFO @ Tue, 10 Dec 2019 13:30:11: 30000000 INFO @ Tue, 10 Dec 2019 13:30:16: 16000000 INFO @ Tue, 10 Dec 2019 13:30:19: 31000000 INFO @ Tue, 10 Dec 2019 13:30:21: 18000000 INFO @ Tue, 10 Dec 2019 13:30:26: 17000000 INFO @ Tue, 10 Dec 2019 13:30:27: 32000000 INFO @ Tue, 10 Dec 2019 13:30:32: 19000000 INFO @ Tue, 10 Dec 2019 13:30:34: 33000000 INFO @ Tue, 10 Dec 2019 13:30:37: 18000000 INFO @ Tue, 10 Dec 2019 13:30:43: 34000000 INFO @ Tue, 10 Dec 2019 13:30:43: 20000000 INFO @ Tue, 10 Dec 2019 13:30:47: 19000000 INFO @ Tue, 10 Dec 2019 13:30:51: 35000000 INFO @ Tue, 10 Dec 2019 13:30:54: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:30:54: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:30:54: #1 total tags in treatment: 35339198 INFO @ Tue, 10 Dec 2019 13:30:54: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:30:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:30:54: #1 tags after filtering in treatment: 35339124 INFO @ Tue, 10 Dec 2019 13:30:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:30:54: #1 finished! INFO @ Tue, 10 Dec 2019 13:30:54: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:30:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:30:55: 21000000 INFO @ Tue, 10 Dec 2019 13:30:58: 20000000 INFO @ Tue, 10 Dec 2019 13:30:58: #2 number of paired peaks: 5747 INFO @ Tue, 10 Dec 2019 13:30:58: start model_add_line... INFO @ Tue, 10 Dec 2019 13:30:59: start X-correlation... INFO @ Tue, 10 Dec 2019 13:30:59: end of X-cor INFO @ Tue, 10 Dec 2019 13:30:59: #2 finished! INFO @ Tue, 10 Dec 2019 13:30:59: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 13:30:59: #2 alternative fragment length(s) may be 50,212,411 bps INFO @ Tue, 10 Dec 2019 13:30:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.05_model.r WARNING @ Tue, 10 Dec 2019 13:30:59: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:30:59: #2 You may need to consider one of the other alternative d(s): 50,212,411 WARNING @ Tue, 10 Dec 2019 13:30:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:30:59: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:30:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:31:06: 22000000 INFO @ Tue, 10 Dec 2019 13:31:09: 21000000 INFO @ Tue, 10 Dec 2019 13:31:17: 23000000 INFO @ Tue, 10 Dec 2019 13:31:19: 22000000 INFO @ Tue, 10 Dec 2019 13:31:29: 24000000 INFO @ Tue, 10 Dec 2019 13:31:30: 23000000 INFO @ Tue, 10 Dec 2019 13:31:40: 25000000 INFO @ Tue, 10 Dec 2019 13:31:40: 24000000 INFO @ Tue, 10 Dec 2019 13:31:51: 25000000 INFO @ Tue, 10 Dec 2019 13:31:51: 26000000 INFO @ Tue, 10 Dec 2019 13:32:01: 26000000 INFO @ Tue, 10 Dec 2019 13:32:03: 27000000 INFO @ Tue, 10 Dec 2019 13:32:12: 27000000 INFO @ Tue, 10 Dec 2019 13:32:14: 28000000 INFO @ Tue, 10 Dec 2019 13:32:22: 28000000 INFO @ Tue, 10 Dec 2019 13:32:25: 29000000 INFO @ Tue, 10 Dec 2019 13:32:33: 29000000 INFO @ Tue, 10 Dec 2019 13:32:36: 30000000 INFO @ Tue, 10 Dec 2019 13:32:43: 30000000 INFO @ Tue, 10 Dec 2019 13:32:48: 31000000 INFO @ Tue, 10 Dec 2019 13:32:49: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:32:53: 31000000 INFO @ Tue, 10 Dec 2019 13:32:59: 32000000 INFO @ Tue, 10 Dec 2019 13:33:04: 32000000 INFO @ Tue, 10 Dec 2019 13:33:10: 33000000 INFO @ Tue, 10 Dec 2019 13:33:14: 33000000 INFO @ Tue, 10 Dec 2019 13:33:22: 34000000 INFO @ Tue, 10 Dec 2019 13:33:25: 34000000 INFO @ Tue, 10 Dec 2019 13:33:34: 35000000 INFO @ Tue, 10 Dec 2019 13:33:36: 35000000 INFO @ Tue, 10 Dec 2019 13:33:39: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:33:39: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:33:39: #1 total tags in treatment: 35339198 INFO @ Tue, 10 Dec 2019 13:33:39: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:33:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:33:40: #1 tags after filtering in treatment: 35339124 INFO @ Tue, 10 Dec 2019 13:33:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:33:40: #1 finished! INFO @ Tue, 10 Dec 2019 13:33:40: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:33:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:33:40: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:33:40: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:33:40: #1 total tags in treatment: 35339198 INFO @ Tue, 10 Dec 2019 13:33:40: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:33:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:33:41: #1 tags after filtering in treatment: 35339124 INFO @ Tue, 10 Dec 2019 13:33:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:33:41: #1 finished! INFO @ Tue, 10 Dec 2019 13:33:41: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:33:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:33:44: #2 number of paired peaks: 5747 INFO @ Tue, 10 Dec 2019 13:33:44: start model_add_line... INFO @ Tue, 10 Dec 2019 13:33:44: start X-correlation... INFO @ Tue, 10 Dec 2019 13:33:44: end of X-cor INFO @ Tue, 10 Dec 2019 13:33:44: #2 finished! INFO @ Tue, 10 Dec 2019 13:33:44: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 13:33:44: #2 alternative fragment length(s) may be 50,212,411 bps INFO @ Tue, 10 Dec 2019 13:33:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.10_model.r WARNING @ Tue, 10 Dec 2019 13:33:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:33:44: #2 You may need to consider one of the other alternative d(s): 50,212,411 WARNING @ Tue, 10 Dec 2019 13:33:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:33:44: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:33:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:33:45: #2 number of paired peaks: 5747 INFO @ Tue, 10 Dec 2019 13:33:45: start model_add_line... INFO @ Tue, 10 Dec 2019 13:33:45: start X-correlation... INFO @ Tue, 10 Dec 2019 13:33:45: end of X-cor INFO @ Tue, 10 Dec 2019 13:33:45: #2 finished! INFO @ Tue, 10 Dec 2019 13:33:45: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 13:33:45: #2 alternative fragment length(s) may be 50,212,411 bps INFO @ Tue, 10 Dec 2019 13:33:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.20_model.r WARNING @ Tue, 10 Dec 2019 13:33:45: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:33:45: #2 You may need to consider one of the other alternative d(s): 50,212,411 WARNING @ Tue, 10 Dec 2019 13:33:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:33:45: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:33:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:33:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:33:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:33:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.05_summits.bed INFO @ Tue, 10 Dec 2019 13:33:46: Done! pass1 - making usageList (49 chroms): 3 millis pass2 - checking and writing primary data (2080 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:35:34: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:35:34: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:36:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:36:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.20_summits.bed INFO @ Tue, 10 Dec 2019 13:36:30: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (575 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:36:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:36:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:36:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779821/SRX4779821.10_summits.bed INFO @ Tue, 10 Dec 2019 13:36:32: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (1186 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。