[2023-06-28 04:20:09,445] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:20:09,448] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:20:09,448] [INFO] DQC Reference Directory: /var/lib/cwl/stgbff97ce2-19d0-42ce-bfe8-70e504f28d68/dqc_reference
[2023-06-28 04:20:11,881] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:20:11,882] [INFO] Task started: Prodigal
[2023-06-28 04:20:11,882] [INFO] Running command: gunzip -c /var/lib/cwl/stga910472b-3919-4717-aab8-89022e3535d1/GCA_019310945.1_ASM1931094v1_genomic.fna.gz | prodigal -d GCA_019310945.1_ASM1931094v1_genomic.fna/cds.fna -a GCA_019310945.1_ASM1931094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:20:19,997] [INFO] Task succeeded: Prodigal
[2023-06-28 04:20:19,997] [INFO] Task started: HMMsearch
[2023-06-28 04:20:19,998] [INFO] Running command: hmmsearch --tblout GCA_019310945.1_ASM1931094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbff97ce2-19d0-42ce-bfe8-70e504f28d68/dqc_reference/reference_markers.hmm GCA_019310945.1_ASM1931094v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:20:20,312] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:20:20,314] [INFO] Found 6/6 markers.
[2023-06-28 04:20:20,350] [INFO] Query marker FASTA was written to GCA_019310945.1_ASM1931094v1_genomic.fna/markers.fasta
[2023-06-28 04:20:20,351] [INFO] Task started: Blastn
[2023-06-28 04:20:20,351] [INFO] Running command: blastn -query GCA_019310945.1_ASM1931094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbff97ce2-19d0-42ce-bfe8-70e504f28d68/dqc_reference/reference_markers.fasta -out GCA_019310945.1_ASM1931094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:20:21,037] [INFO] Task succeeded: Blastn
[2023-06-28 04:20:21,042] [INFO] Selected 28 target genomes.
[2023-06-28 04:20:21,043] [INFO] Target genome list was writen to GCA_019310945.1_ASM1931094v1_genomic.fna/target_genomes.txt
[2023-06-28 04:20:21,051] [INFO] Task started: fastANI
[2023-06-28 04:20:21,052] [INFO] Running command: fastANI --query /var/lib/cwl/stga910472b-3919-4717-aab8-89022e3535d1/GCA_019310945.1_ASM1931094v1_genomic.fna.gz --refList GCA_019310945.1_ASM1931094v1_genomic.fna/target_genomes.txt --output GCA_019310945.1_ASM1931094v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:20:46,376] [INFO] Task succeeded: fastANI
[2023-06-28 04:20:46,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbff97ce2-19d0-42ce-bfe8-70e504f28d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:20:46,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbff97ce2-19d0-42ce-bfe8-70e504f28d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:20:46,391] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:20:46,392] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 04:20:46,392] [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
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.3815	94	774	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.3357	56	774	95	below_threshold
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	75.1057	83	774	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	75.1004	89	774	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	75.0933	90	774	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	75.0634	66	774	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.9928	136	774	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	74.9722	98	774	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	74.94	54	774	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	74.9109	54	774	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.9011	66	774	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	74.874	126	774	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	74.8528	134	774	95	below_threshold
Modestobacter caceresii	strain=KNN 45-2b	GCA_000761485.1	1522368	1522368	type	True	74.8181	77	774	95	below_threshold
Pseudonocardia autotrophica	strain=NBRC 12743	GCA_003945385.1	2074	2074	suspected-type	True	74.681	98	774	95	below_threshold
Pseudonocardia autotrophica	strain=DSM 535	GCA_002119215.1	2074	2074	suspected-type	True	74.6764	99	774	95	below_threshold
Fodinicola acaciae	strain=GKU 173	GCA_010993745.1	2681555	2681555	type	True	74.6677	76	774	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 04:20:46,394] [INFO] DFAST Taxonomy check result was written to GCA_019310945.1_ASM1931094v1_genomic.fna/tc_result.tsv
[2023-06-28 04:20:46,395] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:20:46,395] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:20:46,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbff97ce2-19d0-42ce-bfe8-70e504f28d68/dqc_reference/checkm_data
[2023-06-28 04:20:46,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:20:46,438] [INFO] Task started: CheckM
[2023-06-28 04:20:46,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310945.1_ASM1931094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310945.1_ASM1931094v1_genomic.fna/checkm_input GCA_019310945.1_ASM1931094v1_genomic.fna/checkm_result
[2023-06-28 04:21:13,919] [INFO] Task succeeded: CheckM
[2023-06-28 04:21:13,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:21:13,964] [INFO] ===== Completeness check finished =====
[2023-06-28 04:21:13,964] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:21:13,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310945.1_ASM1931094v1_genomic.fna/markers.fasta)
[2023-06-28 04:21:13,965] [INFO] Task started: Blastn
[2023-06-28 04:21:13,965] [INFO] Running command: blastn -query GCA_019310945.1_ASM1931094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbff97ce2-19d0-42ce-bfe8-70e504f28d68/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310945.1_ASM1931094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:21:14,969] [INFO] Task succeeded: Blastn
[2023-06-28 04:21:14,974] [INFO] Selected 23 target genomes.
[2023-06-28 04:21:14,974] [INFO] Target genome list was writen to GCA_019310945.1_ASM1931094v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:21:14,993] [INFO] Task started: fastANI
[2023-06-28 04:21:14,993] [INFO] Running command: fastANI --query /var/lib/cwl/stga910472b-3919-4717-aab8-89022e3535d1/GCA_019310945.1_ASM1931094v1_genomic.fna.gz --refList GCA_019310945.1_ASM1931094v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310945.1_ASM1931094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:21:30,513] [INFO] Task succeeded: fastANI
[2023-06-28 04:21:30,534] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 04:21:30,535] [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_002687015.1	s__GCA-2687015 sp002687015	76.9874	192	774	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_003576805.1	s__PR03 sp003576805	76.9053	225	774	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_013215615.1	s__JABSQX01 sp013215615	76.8261	129	774	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_016875395.1	s__VGRF01 sp016875395	76.5247	140	774	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	76.4973	149	774	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_002729515.1	s__GCA-2729515 sp002729515	76.4929	111	774	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_905339255.1	s__MYXO sp905339255	76.4322	105	774	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA9160;g__MYXO	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	76.4319	204	774	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_018262315.1	s__PR03 sp018262315	76.239	136	774	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_013215605.1	s__JABSQW01 sp013215605	76.1121	136	774	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_016875225.1	s__VGRW01 sp016875225	76.1057	111	774	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	-
GCA_016713665.1	s__JADJOR01 sp016713665	75.9154	141	774	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_009908425.1	s__JAAAPF01 sp009908425	74.9845	60	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__JAAAPF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709205.1	s__JACCQO01 sp015709205	74.9323	75	774	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__JACCQO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000017645.1	s__Xanthobacter autotrophicus	74.8851	67	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135735.1	s__Sorangium cellulosum_F	74.8099	127	774	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015390235.1	s__Quadrisphaera sp015390235	74.6116	78	774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 04:21:30,537] [INFO] GTDB search result was written to GCA_019310945.1_ASM1931094v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:21:30,537] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:21:30,541] [INFO] DFAST_QC result json was written to GCA_019310945.1_ASM1931094v1_genomic.fna/dqc_result.json
[2023-06-28 04:21:30,542] [INFO] DFAST_QC completed!
[2023-06-28 04:21:30,542] [INFO] Total running time: 0h1m21s