[2023-06-05 18:02:46,870] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:02:46,890] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:02:46,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg93b0589a-a279-4c79-87e6-b6ecf75a032b/dqc_reference
[2023-06-05 18:02:48,505] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:02:48,506] [INFO] Task started: Prodigal
[2023-06-05 18:02:48,507] [INFO] Running command: gunzip -c /var/lib/cwl/stg8214b91c-8b54-4051-a3e1-2c480be077db/GCA_934630945.1_ERR7738160_bin.4_genomic.fna.gz | prodigal -d GCA_934630945.1_ERR7738160_bin.4_genomic.fna/cds.fna -a GCA_934630945.1_ERR7738160_bin.4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:02:53,939] [INFO] Task succeeded: Prodigal
[2023-06-05 18:02:53,940] [INFO] Task started: HMMsearch
[2023-06-05 18:02:53,940] [INFO] Running command: hmmsearch --tblout GCA_934630945.1_ERR7738160_bin.4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93b0589a-a279-4c79-87e6-b6ecf75a032b/dqc_reference/reference_markers.hmm GCA_934630945.1_ERR7738160_bin.4_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:02:54,084] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:02:54,085] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8214b91c-8b54-4051-a3e1-2c480be077db/GCA_934630945.1_ERR7738160_bin.4_genomic.fna.gz]
[2023-06-05 18:02:54,106] [INFO] Query marker FASTA was written to GCA_934630945.1_ERR7738160_bin.4_genomic.fna/markers.fasta
[2023-06-05 18:02:54,106] [INFO] Task started: Blastn
[2023-06-05 18:02:54,106] [INFO] Running command: blastn -query GCA_934630945.1_ERR7738160_bin.4_genomic.fna/markers.fasta -db /var/lib/cwl/stg93b0589a-a279-4c79-87e6-b6ecf75a032b/dqc_reference/reference_markers.fasta -out GCA_934630945.1_ERR7738160_bin.4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:54,601] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:54,605] [INFO] Selected 15 target genomes.
[2023-06-05 18:02:54,605] [INFO] Target genome list was writen to GCA_934630945.1_ERR7738160_bin.4_genomic.fna/target_genomes.txt
[2023-06-05 18:02:54,609] [INFO] Task started: fastANI
[2023-06-05 18:02:54,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg8214b91c-8b54-4051-a3e1-2c480be077db/GCA_934630945.1_ERR7738160_bin.4_genomic.fna.gz --refList GCA_934630945.1_ERR7738160_bin.4_genomic.fna/target_genomes.txt --output GCA_934630945.1_ERR7738160_bin.4_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:03:10,795] [INFO] Task succeeded: fastANI
[2023-06-05 18:03:10,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93b0589a-a279-4c79-87e6-b6ecf75a032b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:03:10,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93b0589a-a279-4c79-87e6-b6ecf75a032b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:03:10,804] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:03:10,804] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:03:10,804] [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	80.0203	207	441	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	79.2167	146	441	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	79.1345	108	441	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.2099	116	441	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.5836	71	441	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.5184	72	441	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:03:10,807] [INFO] DFAST Taxonomy check result was written to GCA_934630945.1_ERR7738160_bin.4_genomic.fna/tc_result.tsv
[2023-06-05 18:03:10,807] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:03:10,808] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:03:10,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93b0589a-a279-4c79-87e6-b6ecf75a032b/dqc_reference/checkm_data
[2023-06-05 18:03:10,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:03:10,838] [INFO] Task started: CheckM
[2023-06-05 18:03:10,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934630945.1_ERR7738160_bin.4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934630945.1_ERR7738160_bin.4_genomic.fna/checkm_input GCA_934630945.1_ERR7738160_bin.4_genomic.fna/checkm_result
[2023-06-05 18:03:34,206] [INFO] Task succeeded: CheckM
[2023-06-05 18:03:34,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:03:34,323] [INFO] ===== Completeness check finished =====
[2023-06-05 18:03:34,323] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:03:34,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934630945.1_ERR7738160_bin.4_genomic.fna/markers.fasta)
[2023-06-05 18:03:34,324] [INFO] Task started: Blastn
[2023-06-05 18:03:34,324] [INFO] Running command: blastn -query GCA_934630945.1_ERR7738160_bin.4_genomic.fna/markers.fasta -db /var/lib/cwl/stg93b0589a-a279-4c79-87e6-b6ecf75a032b/dqc_reference/reference_markers_gtdb.fasta -out GCA_934630945.1_ERR7738160_bin.4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:03:35,403] [INFO] Task succeeded: Blastn
[2023-06-05 18:03:35,407] [INFO] Selected 8 target genomes.
[2023-06-05 18:03:35,407] [INFO] Target genome list was writen to GCA_934630945.1_ERR7738160_bin.4_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:03:35,413] [INFO] Task started: fastANI
[2023-06-05 18:03:35,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg8214b91c-8b54-4051-a3e1-2c480be077db/GCA_934630945.1_ERR7738160_bin.4_genomic.fna.gz --refList GCA_934630945.1_ERR7738160_bin.4_genomic.fna/target_genomes_gtdb.txt --output GCA_934630945.1_ERR7738160_bin.4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:03:41,010] [INFO] Task succeeded: fastANI
[2023-06-05 18:03:41,019] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:03:41,019] [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_900545585.1	s__CAG-83 sp900545585	97.171	388	441	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	conclusive
GCA_900550585.1	s__CAG-83 sp900550585	88.0307	294	441	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_900551355.1	s__CAG-83 sp900551355	87.9211	245	441	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_900547745.1	s__CAG-83 sp900547745	87.3416	285	441	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	-
GCA_900545495.1	s__CAG-83 sp900545495	87.0385	288	441	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_003487665.1	s__CAG-83 sp003487665	83.2437	243	441	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	82.4667	239	441	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_000435975.1	s__CAG-83 sp000435975	80.0805	178	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.04	97.67	0.83	0.76	8	-
--------------------------------------------------------------------------------
[2023-06-05 18:03:41,021] [INFO] GTDB search result was written to GCA_934630945.1_ERR7738160_bin.4_genomic.fna/result_gtdb.tsv
[2023-06-05 18:03:41,022] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:03:41,040] [INFO] DFAST_QC result json was written to GCA_934630945.1_ERR7738160_bin.4_genomic.fna/dqc_result.json
[2023-06-05 18:03:41,040] [INFO] DFAST_QC completed!
[2023-06-05 18:03:41,040] [INFO] Total running time: 0h0m54s