[2023-06-13 20:23:38,321] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:23:38,324] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:23:38,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg97a69f27-31e2-4ea3-aa92-d50e70372b48/dqc_reference
[2023-06-13 20:23:39,615] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:23:39,616] [INFO] Task started: Prodigal
[2023-06-13 20:23:39,616] [INFO] Running command: gunzip -c /var/lib/cwl/stg4eb1616b-1165-4268-8390-92837e510921/GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:23:51,751] [INFO] Task succeeded: Prodigal
[2023-06-13 20:23:51,752] [INFO] Task started: HMMsearch
[2023-06-13 20:23:51,752] [INFO] Running command: hmmsearch --tblout GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97a69f27-31e2-4ea3-aa92-d50e70372b48/dqc_reference/reference_markers.hmm GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:23:51,987] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:23:51,989] [INFO] Found 6/6 markers.
[2023-06-13 20:23:52,025] [INFO] Query marker FASTA was written to GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 20:23:52,026] [INFO] Task started: Blastn
[2023-06-13 20:23:52,026] [INFO] Running command: blastn -query GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg97a69f27-31e2-4ea3-aa92-d50e70372b48/dqc_reference/reference_markers.fasta -out GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:23:52,628] [INFO] Task succeeded: Blastn
[2023-06-13 20:23:52,632] [INFO] Selected 22 target genomes.
[2023-06-13 20:23:52,633] [INFO] Target genome list was writen to GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 20:23:52,684] [INFO] Task started: fastANI
[2023-06-13 20:23:52,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg4eb1616b-1165-4268-8390-92837e510921/GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:24:11,617] [INFO] Task succeeded: fastANI
[2023-06-13 20:24:11,617] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97a69f27-31e2-4ea3-aa92-d50e70372b48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:24:11,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97a69f27-31e2-4ea3-aa92-d50e70372b48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:24:11,627] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 20:24:11,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 20:24:11,627] [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
Victivallis vadensis	strain=DSM 14823	GCA_003096415.1	172901	172901	type	True	98.4089	1366	1576	95	conclusive
Victivallis lenta	strain=BBE-744-WT-12	GCA_009695545.1	2606640	2606640	type	True	80.3737	561	1576	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	74.9322	85	1576	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	74.8498	56	1576	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	74.7833	70	1576	95	below_threshold
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	74.6929	81	1576	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	74.6888	82	1576	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	74.6822	84	1576	95	below_threshold
Nocardia asteroides	strain=NCTC11293	GCA_900637185.1	1824	1824	suspected-type	True	74.6822	84	1576	95	below_threshold
Nocardia rhizosphaerihabitans	strain=CGMCC 4.7329	GCA_014646295.1	1691570	1691570	type	True	74.605	61	1576	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 20:24:11,630] [INFO] DFAST Taxonomy check result was written to GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 20:24:11,631] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:24:11,631] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:24:11,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97a69f27-31e2-4ea3-aa92-d50e70372b48/dqc_reference/checkm_data
[2023-06-13 20:24:11,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:24:11,677] [INFO] Task started: CheckM
[2023-06-13 20:24:11,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 20:24:48,881] [INFO] Task succeeded: CheckM
[2023-06-13 20:24:48,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 20:24:48,900] [INFO] ===== Completeness check finished =====
[2023-06-13 20:24:48,900] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:24:48,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 20:24:48,901] [INFO] Task started: Blastn
[2023-06-13 20:24:48,901] [INFO] Running command: blastn -query GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg97a69f27-31e2-4ea3-aa92-d50e70372b48/dqc_reference/reference_markers_gtdb.fasta -out GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:24:49,797] [INFO] Task succeeded: Blastn
[2023-06-13 20:24:49,801] [INFO] Selected 9 target genomes.
[2023-06-13 20:24:49,801] [INFO] Target genome list was writen to GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:24:49,806] [INFO] Task started: fastANI
[2023-06-13 20:24:49,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg4eb1616b-1165-4268-8390-92837e510921/GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:24:57,984] [INFO] Task succeeded: fastANI
[2023-06-13 20:24:57,992] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 20:24:57,992] [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
GCF_003096415.1	s__Victivallis vadensis	98.4089	1366	1576	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	98.78	98.45	0.89	0.85	7	conclusive
GCF_009695545.1	s__Victivallis lenta	80.3803	560	1576	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	98.99	98.42	0.92	0.87	10	-
GCA_900551245.1	s__Victivallis sp900551245	79.8638	468	1576	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	98.16	98.16	0.84	0.84	2	-
GCA_900550905.1	s__Victivallis sp900550905	79.2096	407	1576	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900768515.1	s__Victivallis sp900768515	78.9002	366	1576	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	99.40	99.40	0.89	0.89	2	-
GCA_018265615.1	s__Victivallis sp018265615	78.8689	503	1576	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761715.1	s__Victivallis sp900761715	78.2432	233	1576	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 20:24:57,994] [INFO] GTDB search result was written to GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 20:24:57,994] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:24:57,997] [INFO] DFAST_QC result json was written to GCA_930980545.1_ERR3414580_bin.83_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 20:24:57,998] [INFO] DFAST_QC completed!
[2023-06-13 20:24:57,998] [INFO] Total running time: 0h1m20s