[2023-06-18 18:53:01,956] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:53:01,959] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:53:01,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg45bb699b-a71e-4b5c-921f-2d53bb1302cc/dqc_reference
[2023-06-18 18:53:04,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:53:04,229] [INFO] Task started: Prodigal
[2023-06-18 18:53:04,229] [INFO] Running command: gunzip -c /var/lib/cwl/stg22f29649-6ded-4336-8c7d-d8ab989175b2/GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:53:11,431] [INFO] Task succeeded: Prodigal
[2023-06-18 18:53:11,431] [INFO] Task started: HMMsearch
[2023-06-18 18:53:11,431] [INFO] Running command: hmmsearch --tblout GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45bb699b-a71e-4b5c-921f-2d53bb1302cc/dqc_reference/reference_markers.hmm GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:53:11,703] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:53:11,704] [INFO] Found 6/6 markers.
[2023-06-18 18:53:11,734] [INFO] Query marker FASTA was written to GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 18:53:11,734] [INFO] Task started: Blastn
[2023-06-18 18:53:11,734] [INFO] Running command: blastn -query GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg45bb699b-a71e-4b5c-921f-2d53bb1302cc/dqc_reference/reference_markers.fasta -out GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:53:12,375] [INFO] Task succeeded: Blastn
[2023-06-18 18:53:12,380] [INFO] Selected 33 target genomes.
[2023-06-18 18:53:12,380] [INFO] Target genome list was writen to GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 18:53:12,382] [INFO] Task started: fastANI
[2023-06-18 18:53:12,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg22f29649-6ded-4336-8c7d-d8ab989175b2/GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:53:31,967] [INFO] Task succeeded: fastANI
[2023-06-18 18:53:31,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45bb699b-a71e-4b5c-921f-2d53bb1302cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:53:31,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45bb699b-a71e-4b5c-921f-2d53bb1302cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:53:31,983] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:53:31,983] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:53:31,983] [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
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	77.1378	78	970	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	77.0774	84	970	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	77.0307	79	970	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.8897	95	970	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.8606	91	970	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	76.7769	50	970	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.7206	65	970	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.6746	51	970	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	76.2887	50	970	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	75.7406	50	970	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:53:31,985] [INFO] DFAST Taxonomy check result was written to GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 18:53:31,985] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:53:31,986] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:53:31,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45bb699b-a71e-4b5c-921f-2d53bb1302cc/dqc_reference/checkm_data
[2023-06-18 18:53:31,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:53:32,022] [INFO] Task started: CheckM
[2023-06-18 18:53:32,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 18:53:58,812] [INFO] Task succeeded: CheckM
[2023-06-18 18:53:58,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:53:58,841] [INFO] ===== Completeness check finished =====
[2023-06-18 18:53:58,842] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:53:58,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 18:53:58,842] [INFO] Task started: Blastn
[2023-06-18 18:53:58,842] [INFO] Running command: blastn -query GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg45bb699b-a71e-4b5c-921f-2d53bb1302cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:53:59,916] [INFO] Task succeeded: Blastn
[2023-06-18 18:53:59,921] [INFO] Selected 17 target genomes.
[2023-06-18 18:53:59,922] [INFO] Target genome list was writen to GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:53:59,931] [INFO] Task started: fastANI
[2023-06-18 18:53:59,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg22f29649-6ded-4336-8c7d-d8ab989175b2/GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:54:09,007] [INFO] Task succeeded: fastANI
[2023-06-18 18:54:09,025] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:54:09,026] [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_900542015.1	s__UBA2882 sp900542015	100.0	967	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	99.84	99.68	0.97	0.94	3	conclusive
GCA_017936785.1	s__UBA2882 sp017936785	80.6457	513	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002362385.1	s__UBA2882 sp002362385	79.4376	374	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	97.70	97.70	0.81	0.81	3	-
GCA_910574745.1	s__UBA2882 sp910574745	79.2416	379	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	99.46	98.95	0.92	0.87	3	-
GCA_900317505.1	s__UBA2882 sp900317505	78.2055	162	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	99.59	99.48	0.89	0.88	4	-
GCA_017387565.1	s__UBA2882 sp017387565	78.1691	168	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578475.1	s__UBA3282 sp910578475	77.1826	90	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465095.1	s__CAG-194 sp017465095	77.138	100	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-194	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018384375.1	s__CAG-95 sp018384375	76.8993	84	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.73	98.22	0.80	0.77	3	-
GCA_017626325.1	s__UBA3282 sp017626325	76.8061	106	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432915.1	s__CAG-194 sp000432915	76.7758	107	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-194	95.0	98.48	96.83	0.89	0.83	7	-
GCA_910579735.1	s__UBA3282 sp910579735	76.6499	102	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586615.1	s__UBA3282 sp910586615	76.5401	89	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550285.1	s__Eisenbergiella sp900550285	76.4994	77	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	99.00	98.94	0.88	0.81	4	-
GCA_003611805.1	s__UBA3282 sp003611805	76.4623	90	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.73	98.68	0.87	0.86	4	-
--------------------------------------------------------------------------------
[2023-06-18 18:54:09,028] [INFO] GTDB search result was written to GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 18:54:09,028] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:54:09,032] [INFO] DFAST_QC result json was written to GCA_937997865.1_ERR1305894_bin.82_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 18:54:09,032] [INFO] DFAST_QC completed!
[2023-06-18 18:54:09,032] [INFO] Total running time: 0h1m7s