[2023-06-28 19:03:55,508] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:03:55,522] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:03:55,523] [INFO] DQC Reference Directory: /var/lib/cwl/stg3dba1f5f-226d-49c2-994a-8908693d0a81/dqc_reference
[2023-06-28 19:03:56,907] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:03:56,907] [INFO] Task started: Prodigal
[2023-06-28 19:03:56,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg727a829b-96c0-4945-8d46-5580b00173fd/GCA_019310975.1_ASM1931097v1_genomic.fna.gz | prodigal -d GCA_019310975.1_ASM1931097v1_genomic.fna/cds.fna -a GCA_019310975.1_ASM1931097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:04:10,943] [INFO] Task succeeded: Prodigal
[2023-06-28 19:04:10,944] [INFO] Task started: HMMsearch
[2023-06-28 19:04:10,944] [INFO] Running command: hmmsearch --tblout GCA_019310975.1_ASM1931097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3dba1f5f-226d-49c2-994a-8908693d0a81/dqc_reference/reference_markers.hmm GCA_019310975.1_ASM1931097v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:04:11,276] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:04:11,277] [INFO] Found 6/6 markers.
[2023-06-28 19:04:11,321] [INFO] Query marker FASTA was written to GCA_019310975.1_ASM1931097v1_genomic.fna/markers.fasta
[2023-06-28 19:04:11,321] [INFO] Task started: Blastn
[2023-06-28 19:04:11,322] [INFO] Running command: blastn -query GCA_019310975.1_ASM1931097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3dba1f5f-226d-49c2-994a-8908693d0a81/dqc_reference/reference_markers.fasta -out GCA_019310975.1_ASM1931097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:04:12,170] [INFO] Task succeeded: Blastn
[2023-06-28 19:04:12,174] [INFO] Selected 31 target genomes.
[2023-06-28 19:04:12,175] [INFO] Target genome list was writen to GCA_019310975.1_ASM1931097v1_genomic.fna/target_genomes.txt
[2023-06-28 19:04:12,197] [INFO] Task started: fastANI
[2023-06-28 19:04:12,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg727a829b-96c0-4945-8d46-5580b00173fd/GCA_019310975.1_ASM1931097v1_genomic.fna.gz --refList GCA_019310975.1_ASM1931097v1_genomic.fna/target_genomes.txt --output GCA_019310975.1_ASM1931097v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:04:41,578] [INFO] Task succeeded: fastANI
[2023-06-28 19:04:41,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3dba1f5f-226d-49c2-994a-8908693d0a81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:04:41,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3dba1f5f-226d-49c2-994a-8908693d0a81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:04:41,599] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:04:41,599] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:04:41,599] [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
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	74.9284	63	1548	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	74.8849	69	1548	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	74.8663	98	1548	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.8661	121	1548	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	74.844	51	1548	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	74.8411	53	1548	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	74.8283	102	1548	95	below_threshold
Streptomyces zinciresistens	strain=K42	GCA_000225525.2	1073330	1073330	type	True	74.7876	92	1548	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	74.7715	86	1548	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	74.7682	56	1548	95	below_threshold
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	74.7652	54	1548	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	74.7644	67	1548	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.7602	201	1548	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.7555	206	1548	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.727	103	1548	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	74.6979	86	1548	95	below_threshold
Actinophytocola oryzae	strain=DSM 45499	GCA_004364325.1	502181	502181	type	True	74.685	122	1548	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	74.6814	130	1548	95	below_threshold
Streptomyces prunicolor	strain=NBRC 13075	GCA_000367365.1	67348	67348	type	True	74.6779	98	1548	95	below_threshold
Streptomyces nodosus	strain=ATCC 14899	GCA_008704995.1	40318	40318	type	True	74.6259	62	1548	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	74.6143	52	1548	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:04:41,601] [INFO] DFAST Taxonomy check result was written to GCA_019310975.1_ASM1931097v1_genomic.fna/tc_result.tsv
[2023-06-28 19:04:41,602] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:04:41,602] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:04:41,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3dba1f5f-226d-49c2-994a-8908693d0a81/dqc_reference/checkm_data
[2023-06-28 19:04:41,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:04:41,657] [INFO] Task started: CheckM
[2023-06-28 19:04:41,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310975.1_ASM1931097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310975.1_ASM1931097v1_genomic.fna/checkm_input GCA_019310975.1_ASM1931097v1_genomic.fna/checkm_result
[2023-06-28 19:05:24,366] [INFO] Task succeeded: CheckM
[2023-06-28 19:05:24,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:05:24,392] [INFO] ===== Completeness check finished =====
[2023-06-28 19:05:24,393] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:05:24,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310975.1_ASM1931097v1_genomic.fna/markers.fasta)
[2023-06-28 19:05:24,393] [INFO] Task started: Blastn
[2023-06-28 19:05:24,393] [INFO] Running command: blastn -query GCA_019310975.1_ASM1931097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3dba1f5f-226d-49c2-994a-8908693d0a81/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310975.1_ASM1931097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:05:25,836] [INFO] Task succeeded: Blastn
[2023-06-28 19:05:25,840] [INFO] Selected 26 target genomes.
[2023-06-28 19:05:25,841] [INFO] Target genome list was writen to GCA_019310975.1_ASM1931097v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:05:25,855] [INFO] Task started: fastANI
[2023-06-28 19:05:25,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg727a829b-96c0-4945-8d46-5580b00173fd/GCA_019310975.1_ASM1931097v1_genomic.fna.gz --refList GCA_019310975.1_ASM1931097v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310975.1_ASM1931097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:05:44,993] [INFO] Task succeeded: fastANI
[2023-06-28 19:05:45,018] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 19:05:45,018] [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_016713665.1	s__JADJOR01 sp016713665	76.4992	283	1548	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_014240165.1	s__JAZXM01 sp014240165	76.3648	178	1548	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JAZXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687015.1	s__GCA-2687015 sp002687015	76.2317	214	1548	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__GCA-2687015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215615.1	s__JABSQX01 sp013215615	76.0685	157	1548	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	76.0571	201	1548	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_002709835.1	s__UBA4427 sp002709835	76.034	147	1548	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691025.1	s__MED660 sp002691025	75.9956	73	1548	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__MED660	95.0	100.00	100.00	0.97	0.97	2	-
GCA_016875395.1	s__VGRF01 sp016875395	75.9227	194	1548	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_012959865.1	s__JAZXM01 sp012959865	75.9163	116	1548	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JAZXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051925.1	s__UBA4427 sp011051925	75.8993	137	1548	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	75.8926	231	1548	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_003576805.1	s__PR03 sp003576805	75.8888	255	1548	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_003647065.1	s__B10-G4 sp003647065	75.033	52	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__B10-G4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739995.1	s__Giesbergeria granuli	74.939	59	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCA_903912445.1	s__DP16D-bin41 sp903912445	74.8692	63	1548	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__CAIQIC01;g__DP16D-bin41	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264315.1	s__Rhodanobacter fulvus	74.8411	53	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303575.1	s__JAFLCL01 sp017303575	74.7962	143	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__JAFLCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112865.1	s__Dyella marensis	74.7961	63	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016872795.1	s__F1-120-MAGs118 sp016872795	74.7224	61	1548	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903896925.1	s__DP16D-bin41 sp903896925	74.7192	50	1548	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__CAIQIC01;g__DP16D-bin41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773355.1	s__SXTU01 sp009773355	74.7131	59	1548	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.99	99.99	0.98	0.97	3	-
GCA_013360535.1	s__F1-120-MAGs118 sp013360535	74.7037	56	1548	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014857905.1	s__JACYXE01 sp014857905	74.7027	70	1548	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__JACYXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709875.1	s__JADJLZ01 sp016709875	74.6645	116	1548	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:05:45,020] [INFO] GTDB search result was written to GCA_019310975.1_ASM1931097v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:05:45,021] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:05:45,026] [INFO] DFAST_QC result json was written to GCA_019310975.1_ASM1931097v1_genomic.fna/dqc_result.json
[2023-06-28 19:05:45,026] [INFO] DFAST_QC completed!
[2023-06-28 19:05:45,026] [INFO] Total running time: 0h1m50s