[2023-06-13 09:48:30,472] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:48:30,475] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:48:30,475] [INFO] DQC Reference Directory: /var/lib/cwl/stgabad9a9c-6034-420f-b464-fd55efa167a9/dqc_reference
[2023-06-13 09:48:31,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:48:31,675] [INFO] Task started: Prodigal
[2023-06-13 09:48:31,675] [INFO] Running command: gunzip -c /var/lib/cwl/stga89ba6b2-201b-4077-b73a-c1f94843a07b/GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:48:37,752] [INFO] Task succeeded: Prodigal
[2023-06-13 09:48:37,752] [INFO] Task started: HMMsearch
[2023-06-13 09:48:37,752] [INFO] Running command: hmmsearch --tblout GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabad9a9c-6034-420f-b464-fd55efa167a9/dqc_reference/reference_markers.hmm GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:48:37,986] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:48:37,987] [INFO] Found 6/6 markers.
[2023-06-13 09:48:38,011] [INFO] Query marker FASTA was written to GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 09:48:38,011] [INFO] Task started: Blastn
[2023-06-13 09:48:38,011] [INFO] Running command: blastn -query GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgabad9a9c-6034-420f-b464-fd55efa167a9/dqc_reference/reference_markers.fasta -out GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:48:38,700] [INFO] Task succeeded: Blastn
[2023-06-13 09:48:38,705] [INFO] Selected 15 target genomes.
[2023-06-13 09:48:38,705] [INFO] Target genome list was writen to GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 09:48:38,707] [INFO] Task started: fastANI
[2023-06-13 09:48:38,708] [INFO] Running command: fastANI --query /var/lib/cwl/stga89ba6b2-201b-4077-b73a-c1f94843a07b/GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:48:45,850] [INFO] Task succeeded: fastANI
[2023-06-13 09:48:45,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabad9a9c-6034-420f-b464-fd55efa167a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:48:45,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabad9a9c-6034-420f-b464-fd55efa167a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:48:45,865] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:48:45,865] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 09:48:45,865] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	81.3271	331	657	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	80.4894	239	657	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.8963	209	657	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.6126	165	657	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.958	128	657	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.6475	132	657	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.5325	111	657	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.4798	120	657	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.2414	106	657	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	77.0186	70	657	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	76.9385	71	657	95	below_threshold
Sporobacter termitidis	strain=DSM 10068	GCA_900130065.1	44749	44749	type	True	76.0558	54	657	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:48:45,867] [INFO] DFAST Taxonomy check result was written to GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 09:48:45,868] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:48:45,868] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:48:45,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabad9a9c-6034-420f-b464-fd55efa167a9/dqc_reference/checkm_data
[2023-06-13 09:48:45,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:48:45,895] [INFO] Task started: CheckM
[2023-06-13 09:48:45,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 09:49:10,099] [INFO] Task succeeded: CheckM
[2023-06-13 09:49:10,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:49:10,126] [INFO] ===== Completeness check finished =====
[2023-06-13 09:49:10,126] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:49:10,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 09:49:10,127] [INFO] Task started: Blastn
[2023-06-13 09:49:10,127] [INFO] Running command: blastn -query GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgabad9a9c-6034-420f-b464-fd55efa167a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:49:11,511] [INFO] Task succeeded: Blastn
[2023-06-13 09:49:11,515] [INFO] Selected 9 target genomes.
[2023-06-13 09:49:11,516] [INFO] Target genome list was writen to GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:49:11,524] [INFO] Task started: fastANI
[2023-06-13 09:49:11,524] [INFO] Running command: fastANI --query /var/lib/cwl/stga89ba6b2-201b-4077-b73a-c1f94843a07b/GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:49:15,480] [INFO] Task succeeded: fastANI
[2023-06-13 09:49:15,489] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:49:15,489] [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_900547745.1	s__CAG-83 sp900547745	98.9154	493	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.22	99.21	0.93	0.91	3	conclusive
GCA_900551355.1	s__CAG-83 sp900551355	91.6662	344	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.94	98.90	0.93	0.92	3	-
GCA_900550585.1	s__CAG-83 sp900550585	91.2351	430	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.85	99.85	0.92	0.92	2	-
GCA_900545495.1	s__CAG-83 sp900545495	89.2562	432	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.95	95.34	0.89	0.84	5	-
GCA_900545585.1	s__CAG-83 sp900545585	88.5314	449	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.41	98.11	0.88	0.81	5	-
GCA_003487665.1	s__CAG-83 sp003487665	85.1309	355	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.43	97.11	0.80	0.74	11	-
GCA_900554275.1	s__CAG-83 sp900554275	84.3035	333	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.46	96.91	0.80	0.75	4	-
GCA_900551995.1	s__CAG-83 sp900551995	83.8451	334	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.79	97.61	0.85	0.83	3	-
GCA_000435555.1	s__CAG-83 sp000435555	83.1156	324	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.91	97.56	0.88	0.73	17	-
--------------------------------------------------------------------------------
[2023-06-13 09:49:15,493] [INFO] GTDB search result was written to GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 09:49:15,494] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:49:15,502] [INFO] DFAST_QC result json was written to GCA_938014565.1_ERR912155_bin.16_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 09:49:15,503] [INFO] DFAST_QC completed!
[2023-06-13 09:49:15,503] [INFO] Total running time: 0h0m45s