[2023-06-29 14:22:10,416] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:22:10,418] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:22:10,418] [INFO] DQC Reference Directory: /var/lib/cwl/stgeff99802-8066-4ede-9438-451183f077a2/dqc_reference
[2023-06-29 14:22:11,581] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:22:11,582] [INFO] Task started: Prodigal
[2023-06-29 14:22:11,582] [INFO] Running command: gunzip -c /var/lib/cwl/stgd29336ac-e8c9-417e-b0cc-da61c743bf9c/GCA_011322845.1_ASM1132284v1_genomic.fna.gz | prodigal -d GCA_011322845.1_ASM1132284v1_genomic.fna/cds.fna -a GCA_011322845.1_ASM1132284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:22:14,899] [INFO] Task succeeded: Prodigal
[2023-06-29 14:22:14,899] [INFO] Task started: HMMsearch
[2023-06-29 14:22:14,899] [INFO] Running command: hmmsearch --tblout GCA_011322845.1_ASM1132284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeff99802-8066-4ede-9438-451183f077a2/dqc_reference/reference_markers.hmm GCA_011322845.1_ASM1132284v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:22:15,045] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:22:15,046] [INFO] Found 6/6 markers.
[2023-06-29 14:22:15,063] [INFO] Query marker FASTA was written to GCA_011322845.1_ASM1132284v1_genomic.fna/markers.fasta
[2023-06-29 14:22:15,063] [INFO] Task started: Blastn
[2023-06-29 14:22:15,063] [INFO] Running command: blastn -query GCA_011322845.1_ASM1132284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff99802-8066-4ede-9438-451183f077a2/dqc_reference/reference_markers.fasta -out GCA_011322845.1_ASM1132284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:22:15,792] [INFO] Task succeeded: Blastn
[2023-06-29 14:22:15,796] [INFO] Selected 27 target genomes.
[2023-06-29 14:22:15,796] [INFO] Target genome list was writen to GCA_011322845.1_ASM1132284v1_genomic.fna/target_genomes.txt
[2023-06-29 14:22:15,798] [INFO] Task started: fastANI
[2023-06-29 14:22:15,798] [INFO] Running command: fastANI --query /var/lib/cwl/stgd29336ac-e8c9-417e-b0cc-da61c743bf9c/GCA_011322845.1_ASM1132284v1_genomic.fna.gz --refList GCA_011322845.1_ASM1132284v1_genomic.fna/target_genomes.txt --output GCA_011322845.1_ASM1132284v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:22:33,153] [INFO] Task succeeded: fastANI
[2023-06-29 14:22:33,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeff99802-8066-4ede-9438-451183f077a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:22:33,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeff99802-8066-4ede-9438-451183f077a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:22:33,164] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:22:33,164] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:22:33,164] [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
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	77.7543	64	326	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.3413	58	326	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	77.2036	62	326	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	77.1635	68	326	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	77.1518	79	326	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.1202	80	326	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	77.0149	65	326	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.9274	55	326	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.8676	54	326	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.7801	58	326	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.627	62	326	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.2525	51	326	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:22:33,167] [INFO] DFAST Taxonomy check result was written to GCA_011322845.1_ASM1132284v1_genomic.fna/tc_result.tsv
[2023-06-29 14:22:33,167] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:22:33,167] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:22:33,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeff99802-8066-4ede-9438-451183f077a2/dqc_reference/checkm_data
[2023-06-29 14:22:33,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:22:33,186] [INFO] Task started: CheckM
[2023-06-29 14:22:33,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011322845.1_ASM1132284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011322845.1_ASM1132284v1_genomic.fna/checkm_input GCA_011322845.1_ASM1132284v1_genomic.fna/checkm_result
[2023-06-29 14:22:49,213] [INFO] Task succeeded: CheckM
[2023-06-29 14:22:49,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:22:49,239] [INFO] ===== Completeness check finished =====
[2023-06-29 14:22:49,239] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:22:49,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011322845.1_ASM1132284v1_genomic.fna/markers.fasta)
[2023-06-29 14:22:49,240] [INFO] Task started: Blastn
[2023-06-29 14:22:49,240] [INFO] Running command: blastn -query GCA_011322845.1_ASM1132284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff99802-8066-4ede-9438-451183f077a2/dqc_reference/reference_markers_gtdb.fasta -out GCA_011322845.1_ASM1132284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:22:50,479] [INFO] Task succeeded: Blastn
[2023-06-29 14:22:50,483] [INFO] Selected 25 target genomes.
[2023-06-29 14:22:50,484] [INFO] Target genome list was writen to GCA_011322845.1_ASM1132284v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:22:50,493] [INFO] Task started: fastANI
[2023-06-29 14:22:50,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgd29336ac-e8c9-417e-b0cc-da61c743bf9c/GCA_011322845.1_ASM1132284v1_genomic.fna.gz --refList GCA_011322845.1_ASM1132284v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011322845.1_ASM1132284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:23:03,885] [INFO] Task succeeded: fastANI
[2023-06-29 14:23:03,899] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:23:03,900] [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_015494335.1	s__S144-22 sp015494335	78.262	67	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__S144-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	78.0232	56	326	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_012276755.1	s__Marichromatium bheemlicum	77.7543	64	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	77.4992	85	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000801295.1	s__MONJU sp000801295	77.4423	85	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	77.4347	65	326	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_011390365.1	s__SLIM01 sp011390365	77.3406	57	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__SLIM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583835.1	s__Thiococcus pfennigii	77.2873	61	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiococcus	95.0	98.97	98.97	0.88	0.88	2	-
GCF_018409545.1	s__Allochromatium tepidum	77.2036	62	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	77.1518	79	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_013385175.1	s__Allochromatium humboldtianum	77.1286	69	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	77.0149	65	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_009720725.1	s__Allochromatium palmeri	76.991	61	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000327045.1	s__Thioflavicoccus mobilis	76.8676	54	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thioflavicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	76.8139	50	326	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_011051655.1	s__DRKS01 sp011051655	76.7602	65	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696465.1	s__J044 sp003696465	76.7545	51	326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J044;f__J044;g__J044	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	76.2525	51	326	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	-
--------------------------------------------------------------------------------
[2023-06-29 14:23:03,902] [INFO] GTDB search result was written to GCA_011322845.1_ASM1132284v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:23:03,902] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:23:03,906] [INFO] DFAST_QC result json was written to GCA_011322845.1_ASM1132284v1_genomic.fna/dqc_result.json
[2023-06-29 14:23:03,906] [INFO] DFAST_QC completed!
[2023-06-29 14:23:03,906] [INFO] Total running time: 0h0m53s