[2023-06-13 12:04:31,637] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:04:31,640] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:04:31,640] [INFO] DQC Reference Directory: /var/lib/cwl/stg220d6c22-83b5-4188-8716-42ab4d47c4b3/dqc_reference
[2023-06-13 12:04:32,862] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:04:32,863] [INFO] Task started: Prodigal
[2023-06-13 12:04:32,863] [INFO] Running command: gunzip -c /var/lib/cwl/stg2027e553-eb54-4f9b-8e3b-2252fc3ba258/GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:04:40,167] [INFO] Task succeeded: Prodigal
[2023-06-13 12:04:40,168] [INFO] Task started: HMMsearch
[2023-06-13 12:04:40,168] [INFO] Running command: hmmsearch --tblout GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg220d6c22-83b5-4188-8716-42ab4d47c4b3/dqc_reference/reference_markers.hmm GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:04:40,421] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:04:40,423] [INFO] Found 6/6 markers.
[2023-06-13 12:04:40,455] [INFO] Query marker FASTA was written to GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 12:04:40,456] [INFO] Task started: Blastn
[2023-06-13 12:04:40,456] [INFO] Running command: blastn -query GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg220d6c22-83b5-4188-8716-42ab4d47c4b3/dqc_reference/reference_markers.fasta -out GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:04:41,115] [INFO] Task succeeded: Blastn
[2023-06-13 12:04:41,121] [INFO] Selected 28 target genomes.
[2023-06-13 12:04:41,121] [INFO] Target genome list was writen to GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 12:04:41,124] [INFO] Task started: fastANI
[2023-06-13 12:04:41,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg2027e553-eb54-4f9b-8e3b-2252fc3ba258/GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:04:57,407] [INFO] Task succeeded: fastANI
[2023-06-13 12:04:57,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg220d6c22-83b5-4188-8716-42ab4d47c4b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:04:57,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg220d6c22-83b5-4188-8716-42ab4d47c4b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:04:57,423] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 12:04:57,423] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 12:04:57,423] [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
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.2972	67	1012	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.1794	80	1012	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	75.9876	94	1012	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	75.9368	86	1012	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	75.9033	88	1012	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	75.8764	91	1012	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 12:04:57,425] [INFO] DFAST Taxonomy check result was written to GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 12:04:57,426] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:04:57,426] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:04:57,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg220d6c22-83b5-4188-8716-42ab4d47c4b3/dqc_reference/checkm_data
[2023-06-13 12:04:57,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:04:57,463] [INFO] Task started: CheckM
[2023-06-13 12:04:57,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 12:05:24,739] [INFO] Task succeeded: CheckM
[2023-06-13 12:05:24,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 12:05:24,767] [INFO] ===== Completeness check finished =====
[2023-06-13 12:05:24,768] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:05:24,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 12:05:24,768] [INFO] Task started: Blastn
[2023-06-13 12:05:24,769] [INFO] Running command: blastn -query GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg220d6c22-83b5-4188-8716-42ab4d47c4b3/dqc_reference/reference_markers_gtdb.fasta -out GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:05:25,839] [INFO] Task succeeded: Blastn
[2023-06-13 12:05:25,844] [INFO] Selected 14 target genomes.
[2023-06-13 12:05:25,844] [INFO] Target genome list was writen to GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:05:25,848] [INFO] Task started: fastANI
[2023-06-13 12:05:25,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg2027e553-eb54-4f9b-8e3b-2252fc3ba258/GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:05:33,927] [INFO] Task succeeded: fastANI
[2023-06-13 12:05:33,944] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 12:05:33,945] [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_910584965.1	s__UBA3282 sp910584965	81.3382	656	1012	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_910578475.1	s__UBA3282 sp910578475	80.7932	634	1012	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_910578715.1	s__UBA3282 sp910578715	80.7454	620	1012	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_910579395.1	s__UBA3282 sp910579395	80.4031	593	1012	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_910579735.1	s__UBA3282 sp910579735	78.1552	342	1012	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_910578845.1	s__UBA3282 sp910578845	77.3202	274	1012	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_014804695.1	s__UBA3282 sp014804695	77.1118	206	1012	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_017623295.1	s__UBA3282 sp017623295	76.9354	162	1012	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_017440375.1	s__UBA3282 sp017440375	76.8447	110	1012	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_002492525.1	s__UBA3282 sp002492525	76.4332	142	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.83	99.82	0.86	0.82	3	-
GCA_900542015.1	s__UBA2882 sp900542015	75.9943	96	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	99.84	99.68	0.97	0.94	3	-
GCA_910589655.1	s__Acetatifactor sp910589655	75.4252	72	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 12:05:33,947] [INFO] GTDB search result was written to GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 12:05:33,947] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:05:33,950] [INFO] DFAST_QC result json was written to GCA_947086855.1_SRR14038239_bin.32_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 12:05:33,950] [INFO] DFAST_QC completed!
[2023-06-13 12:05:33,950] [INFO] Total running time: 0h1m2s