[2023-06-28 00:20:56,544] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:20:56,546] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:20:56,546] [INFO] DQC Reference Directory: /var/lib/cwl/stgccf3b4ab-30f1-4062-b22f-2f9abda3e5b0/dqc_reference
[2023-06-28 00:20:58,000] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:20:58,002] [INFO] Task started: Prodigal
[2023-06-28 00:20:58,002] [INFO] Running command: gunzip -c /var/lib/cwl/stg1928f719-319b-425c-a9cf-f39cd3ab259f/GCA_019310965.1_ASM1931096v1_genomic.fna.gz | prodigal -d GCA_019310965.1_ASM1931096v1_genomic.fna/cds.fna -a GCA_019310965.1_ASM1931096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:21:11,069] [INFO] Task succeeded: Prodigal
[2023-06-28 00:21:11,070] [INFO] Task started: HMMsearch
[2023-06-28 00:21:11,070] [INFO] Running command: hmmsearch --tblout GCA_019310965.1_ASM1931096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccf3b4ab-30f1-4062-b22f-2f9abda3e5b0/dqc_reference/reference_markers.hmm GCA_019310965.1_ASM1931096v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:21:11,378] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:21:11,379] [INFO] Found 6/6 markers.
[2023-06-28 00:21:11,424] [INFO] Query marker FASTA was written to GCA_019310965.1_ASM1931096v1_genomic.fna/markers.fasta
[2023-06-28 00:21:11,425] [INFO] Task started: Blastn
[2023-06-28 00:21:11,425] [INFO] Running command: blastn -query GCA_019310965.1_ASM1931096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccf3b4ab-30f1-4062-b22f-2f9abda3e5b0/dqc_reference/reference_markers.fasta -out GCA_019310965.1_ASM1931096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:21:12,174] [INFO] Task succeeded: Blastn
[2023-06-28 00:21:12,178] [INFO] Selected 26 target genomes.
[2023-06-28 00:21:12,179] [INFO] Target genome list was writen to GCA_019310965.1_ASM1931096v1_genomic.fna/target_genomes.txt
[2023-06-28 00:21:12,183] [INFO] Task started: fastANI
[2023-06-28 00:21:12,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg1928f719-319b-425c-a9cf-f39cd3ab259f/GCA_019310965.1_ASM1931096v1_genomic.fna.gz --refList GCA_019310965.1_ASM1931096v1_genomic.fna/target_genomes.txt --output GCA_019310965.1_ASM1931096v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:21:35,309] [INFO] Task succeeded: fastANI
[2023-06-28 00:21:35,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccf3b4ab-30f1-4062-b22f-2f9abda3e5b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:21:35,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccf3b4ab-30f1-4062-b22f-2f9abda3e5b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:21:35,330] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:21:35,331] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 00:21:35,331] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.292	55	1474	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	75.1293	98	1474	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.0855	88	1474	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.0831	190	1474	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	75.0691	96	1474	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	75.0039	67	1474	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	74.9909	69	1474	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	74.9824	91	1474	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	74.9475	86	1474	95	below_threshold
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	74.9376	112	1474	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	74.936	108	1474	95	below_threshold
Verticiella sediminum	strain=DSM 27279	GCA_007558815.1	1247510	1247510	type	True	74.8631	88	1474	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	74.8556	96	1474	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	74.8369	121	1474	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	74.8354	121	1474	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.791	93	1474	95	below_threshold
Bordetella parapertussis	strain=NCTC5952	GCA_900445785.1	519	519	suspected-type	True	74.7663	76	1474	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	74.7586	78	1474	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.7551	150	1474	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.7196	96	1474	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	74.6483	73	1474	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	74.6472	74	1474	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:21:35,333] [INFO] DFAST Taxonomy check result was written to GCA_019310965.1_ASM1931096v1_genomic.fna/tc_result.tsv
[2023-06-28 00:21:35,333] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:21:35,333] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:21:35,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccf3b4ab-30f1-4062-b22f-2f9abda3e5b0/dqc_reference/checkm_data
[2023-06-28 00:21:35,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:21:35,382] [INFO] Task started: CheckM
[2023-06-28 00:21:35,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310965.1_ASM1931096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310965.1_ASM1931096v1_genomic.fna/checkm_input GCA_019310965.1_ASM1931096v1_genomic.fna/checkm_result
[2023-06-28 00:22:16,727] [INFO] Task succeeded: CheckM
[2023-06-28 00:22:16,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:22:16,753] [INFO] ===== Completeness check finished =====
[2023-06-28 00:22:16,753] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:22:16,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310965.1_ASM1931096v1_genomic.fna/markers.fasta)
[2023-06-28 00:22:16,754] [INFO] Task started: Blastn
[2023-06-28 00:22:16,754] [INFO] Running command: blastn -query GCA_019310965.1_ASM1931096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccf3b4ab-30f1-4062-b22f-2f9abda3e5b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310965.1_ASM1931096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:22:17,838] [INFO] Task succeeded: Blastn
[2023-06-28 00:22:17,842] [INFO] Selected 17 target genomes.
[2023-06-28 00:22:17,843] [INFO] Target genome list was writen to GCA_019310965.1_ASM1931096v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:22:17,865] [INFO] Task started: fastANI
[2023-06-28 00:22:17,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg1928f719-319b-425c-a9cf-f39cd3ab259f/GCA_019310965.1_ASM1931096v1_genomic.fna.gz --refList GCA_019310965.1_ASM1931096v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310965.1_ASM1931096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:22:30,049] [INFO] Task succeeded: fastANI
[2023-06-28 00:22:30,066] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:22:30,066] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002729515.1	s__GCA-2729515 sp002729515	77.4177	342	1474	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__GCA-2729515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356735.1	s__SMWR01 sp004356735	77.294	183	1474	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__SMWR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	76.8047	280	1474	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.6478	279	1474	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	76.2985	255	1474	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875395.1	s__VGRF01 sp016875395	76.2969	243	1474	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696485.1	s__CAADGG01 sp900696485	76.1181	202	1474	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__CAADGG01	95.0	99.84	99.84	0.91	0.91	2	-
GCA_016713665.1	s__JADJOR01 sp016713665	76.0942	259	1474	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875225.1	s__VGRW01 sp016875225	75.7242	166	1474	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__VGRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016615815.1	s__Luteimonas sp016615815	75.0853	74	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.14	98.29	0.98	0.95	3	-
GCA_017302495.1	s__Rubrivivax sp017302495	75.0763	95	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294065.1	s__Sphaerotilus sp013294065	75.0685	116	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014236855.1	s__Xanthomonas_A sp014236855	75.0326	86	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	95.82	95.01	0.91	0.88	7	-
GCF_014197395.1	s__Xanthomonas_A translucens_B	74.8974	93	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209015.1	s__JACQWY01 sp016209015	74.7779	104	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__JACQWY01	95.0	99.49	99.49	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-28 00:22:30,069] [INFO] GTDB search result was written to GCA_019310965.1_ASM1931096v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:22:30,069] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:22:30,074] [INFO] DFAST_QC result json was written to GCA_019310965.1_ASM1931096v1_genomic.fna/dqc_result.json
[2023-06-28 00:22:30,074] [INFO] DFAST_QC completed!
[2023-06-28 00:22:30,074] [INFO] Total running time: 0h1m34s