[2023-06-28 23:05:49,897] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:05:49,900] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:05:49,900] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5090403-1406-4254-bec9-8b6ef5d6f601/dqc_reference
[2023-06-28 23:05:51,211] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:05:51,211] [INFO] Task started: Prodigal
[2023-06-28 23:05:51,212] [INFO] Running command: gunzip -c /var/lib/cwl/stgafb58a84-428d-4ae6-b80e-200c7f23428e/GCA_015488555.1_ASM1548855v1_genomic.fna.gz | prodigal -d GCA_015488555.1_ASM1548855v1_genomic.fna/cds.fna -a GCA_015488555.1_ASM1548855v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:05:58,449] [INFO] Task succeeded: Prodigal
[2023-06-28 23:05:58,450] [INFO] Task started: HMMsearch
[2023-06-28 23:05:58,450] [INFO] Running command: hmmsearch --tblout GCA_015488555.1_ASM1548855v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5090403-1406-4254-bec9-8b6ef5d6f601/dqc_reference/reference_markers.hmm GCA_015488555.1_ASM1548855v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:05:58,643] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:05:58,645] [INFO] Found 6/6 markers.
[2023-06-28 23:05:58,669] [INFO] Query marker FASTA was written to GCA_015488555.1_ASM1548855v1_genomic.fna/markers.fasta
[2023-06-28 23:05:58,670] [INFO] Task started: Blastn
[2023-06-28 23:05:58,670] [INFO] Running command: blastn -query GCA_015488555.1_ASM1548855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5090403-1406-4254-bec9-8b6ef5d6f601/dqc_reference/reference_markers.fasta -out GCA_015488555.1_ASM1548855v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:05:59,541] [INFO] Task succeeded: Blastn
[2023-06-28 23:05:59,546] [INFO] Selected 26 target genomes.
[2023-06-28 23:05:59,546] [INFO] Target genome list was writen to GCA_015488555.1_ASM1548855v1_genomic.fna/target_genomes.txt
[2023-06-28 23:05:59,550] [INFO] Task started: fastANI
[2023-06-28 23:05:59,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgafb58a84-428d-4ae6-b80e-200c7f23428e/GCA_015488555.1_ASM1548855v1_genomic.fna.gz --refList GCA_015488555.1_ASM1548855v1_genomic.fna/target_genomes.txt --output GCA_015488555.1_ASM1548855v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:06:15,286] [INFO] Task succeeded: fastANI
[2023-06-28 23:06:15,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5090403-1406-4254-bec9-8b6ef5d6f601/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:06:15,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5090403-1406-4254-bec9-8b6ef5d6f601/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:06:15,305] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:06:15,305] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:06:15,305] [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
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.9226	193	712	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.8113	161	712	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.5296	204	712	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	77.4519	164	712	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	77.2153	139	712	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	77.1827	157	712	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.1411	130	712	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	76.9487	105	712	95	below_threshold
Ectothiorhodospira marina	strain=DSM 241	GCA_900109495.1	1396821	1396821	type	True	76.8071	120	712	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	76.7015	99	712	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	76.6987	86	712	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.6899	104	712	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.5055	73	712	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	76.4677	103	712	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	76.4525	94	712	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.3859	110	712	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	76.3481	89	712	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.3403	92	712	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.3296	104	712	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.2533	94	712	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.2169	97	712	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	75.882	58	712	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.8003	73	712	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:06:15,307] [INFO] DFAST Taxonomy check result was written to GCA_015488555.1_ASM1548855v1_genomic.fna/tc_result.tsv
[2023-06-28 23:06:15,308] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:06:15,308] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:06:15,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5090403-1406-4254-bec9-8b6ef5d6f601/dqc_reference/checkm_data
[2023-06-28 23:06:15,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:06:15,335] [INFO] Task started: CheckM
[2023-06-28 23:06:15,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015488555.1_ASM1548855v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015488555.1_ASM1548855v1_genomic.fna/checkm_input GCA_015488555.1_ASM1548855v1_genomic.fna/checkm_result
[2023-06-28 23:06:42,364] [INFO] Task succeeded: CheckM
[2023-06-28 23:06:42,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:06:42,384] [INFO] ===== Completeness check finished =====
[2023-06-28 23:06:42,384] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:06:42,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015488555.1_ASM1548855v1_genomic.fna/markers.fasta)
[2023-06-28 23:06:42,384] [INFO] Task started: Blastn
[2023-06-28 23:06:42,384] [INFO] Running command: blastn -query GCA_015488555.1_ASM1548855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5090403-1406-4254-bec9-8b6ef5d6f601/dqc_reference/reference_markers_gtdb.fasta -out GCA_015488555.1_ASM1548855v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:06:44,027] [INFO] Task succeeded: Blastn
[2023-06-28 23:06:44,032] [INFO] Selected 23 target genomes.
[2023-06-28 23:06:44,032] [INFO] Target genome list was writen to GCA_015488555.1_ASM1548855v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:06:44,037] [INFO] Task started: fastANI
[2023-06-28 23:06:44,037] [INFO] Running command: fastANI --query /var/lib/cwl/stgafb58a84-428d-4ae6-b80e-200c7f23428e/GCA_015488555.1_ASM1548855v1_genomic.fna.gz --refList GCA_015488555.1_ASM1548855v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015488555.1_ASM1548855v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:06:55,510] [INFO] Task succeeded: fastANI
[2023-06-28 23:06:55,528] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:06:55,528] [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_015488555.1	s__S012-109 sp015488555	100.0	701	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-140;f__SZUA-140;g__S012-109	95.0	99.64	99.60	0.87	0.87	3	conclusive
GCA_015492435.1	s__SZUA-140 sp015492435	79.1807	244	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-140;f__SZUA-140;g__SZUA-140	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	77.9222	193	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695825.1	s__J048 sp003695825	77.8852	137	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J048;f__J048;g__J048	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490395.1	s__S141-70 sp015490395	77.8534	136	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S141-70;f__S141-70;g__S141-70	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114895.1	s__Ectothiorhodospira mobilis_A	77.8099	164	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	77.5734	138	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716465.1	s__JADJWH01 sp016716465	77.5655	171	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JADJWH01;f__JADJWH01;g__JADJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	77.5157	205	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051655.1	s__DRKS01 sp011051655	77.4594	129	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	77.4518	164	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	77.4105	128	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCA_015494165.1	s__S144-34 sp015494165	77.3104	140	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000365.1	s__Thioalkalivibrio_A denitrificans	77.2153	139	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013348725.1	s__GCA-013348725 sp013348725	77.0793	134	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-013348725;f__GCA-013348725;g__GCA-013348725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001447805.1	s__Tenderia electrophaga	77.0154	152	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Tenderiales;f__Tenderiaceae;g__Tenderia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011046015.1	s__SpSt-1174 sp011046015	76.9441	88	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378965.1	s__Thioalkalivibrio_A thiocyanodenitrificans	76.702	130	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377405.1	s__Thioalkalivibrio sp000377405	76.5645	93	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.90	97.79	0.93	0.92	11	-
GCF_000327045.1	s__Thioflavicoccus mobilis	76.5055	73	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thioflavicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014337915.1	s__QUBU01 sp014337915	76.257	66	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__QUBU01	95.0	99.72	99.56	0.97	0.95	4	-
GCA_018057015.1	s__UBA5518 sp018057015	76.0097	60	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:06:55,530] [INFO] GTDB search result was written to GCA_015488555.1_ASM1548855v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:06:55,530] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:06:55,536] [INFO] DFAST_QC result json was written to GCA_015488555.1_ASM1548855v1_genomic.fna/dqc_result.json
[2023-06-28 23:06:55,536] [INFO] DFAST_QC completed!
[2023-06-28 23:06:55,536] [INFO] Total running time: 0h1m6s