[2023-06-04 21:24:52,676] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:24:52,821] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:24:52,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg05c5edeb-81fe-4df9-accb-cacf6a3ed5c8/dqc_reference
[2023-06-04 21:24:56,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:24:56,272] [INFO] Task started: Prodigal
[2023-06-04 21:24:56,272] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a719137-e32d-478b-8684-bbbb93f25aa3/GCA_934561065.1_ERR7738643_bin.71_genomic.fna.gz | prodigal -d GCA_934561065.1_ERR7738643_bin.71_genomic.fna/cds.fna -a GCA_934561065.1_ERR7738643_bin.71_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:25:00,963] [INFO] Task succeeded: Prodigal
[2023-06-04 21:25:00,964] [INFO] Task started: HMMsearch
[2023-06-04 21:25:00,964] [INFO] Running command: hmmsearch --tblout GCA_934561065.1_ERR7738643_bin.71_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05c5edeb-81fe-4df9-accb-cacf6a3ed5c8/dqc_reference/reference_markers.hmm GCA_934561065.1_ERR7738643_bin.71_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:25:01,246] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:25:01,248] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7a719137-e32d-478b-8684-bbbb93f25aa3/GCA_934561065.1_ERR7738643_bin.71_genomic.fna.gz]
[2023-06-04 21:25:01,283] [INFO] Query marker FASTA was written to GCA_934561065.1_ERR7738643_bin.71_genomic.fna/markers.fasta
[2023-06-04 21:25:01,284] [INFO] Task started: Blastn
[2023-06-04 21:25:01,284] [INFO] Running command: blastn -query GCA_934561065.1_ERR7738643_bin.71_genomic.fna/markers.fasta -db /var/lib/cwl/stg05c5edeb-81fe-4df9-accb-cacf6a3ed5c8/dqc_reference/reference_markers.fasta -out GCA_934561065.1_ERR7738643_bin.71_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:25:02,260] [INFO] Task succeeded: Blastn
[2023-06-04 21:25:02,264] [INFO] Selected 11 target genomes.
[2023-06-04 21:25:02,265] [INFO] Target genome list was writen to GCA_934561065.1_ERR7738643_bin.71_genomic.fna/target_genomes.txt
[2023-06-04 21:25:02,266] [INFO] Task started: fastANI
[2023-06-04 21:25:02,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a719137-e32d-478b-8684-bbbb93f25aa3/GCA_934561065.1_ERR7738643_bin.71_genomic.fna.gz --refList GCA_934561065.1_ERR7738643_bin.71_genomic.fna/target_genomes.txt --output GCA_934561065.1_ERR7738643_bin.71_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:25:07,355] [INFO] Task succeeded: fastANI
[2023-06-04 21:25:07,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05c5edeb-81fe-4df9-accb-cacf6a3ed5c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:25:07,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05c5edeb-81fe-4df9-accb-cacf6a3ed5c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:25:07,365] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:25:07,365] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 21:25:07,365] [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	80.097	218	499	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	79.362	181	499	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.9566	122	499	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.8828	155	499	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.6296	87	499	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.5007	94	499	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.1574	59	499	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	76.8358	101	499	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 21:25:07,367] [INFO] DFAST Taxonomy check result was written to GCA_934561065.1_ERR7738643_bin.71_genomic.fna/tc_result.tsv
[2023-06-04 21:25:07,368] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:25:07,368] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:25:07,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05c5edeb-81fe-4df9-accb-cacf6a3ed5c8/dqc_reference/checkm_data
[2023-06-04 21:25:07,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:25:07,392] [INFO] Task started: CheckM
[2023-06-04 21:25:07,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934561065.1_ERR7738643_bin.71_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934561065.1_ERR7738643_bin.71_genomic.fna/checkm_input GCA_934561065.1_ERR7738643_bin.71_genomic.fna/checkm_result
[2023-06-04 21:25:27,900] [INFO] Task succeeded: CheckM
[2023-06-04 21:25:27,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 36.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:25:27,954] [INFO] ===== Completeness check finished =====
[2023-06-04 21:25:27,954] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:25:27,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934561065.1_ERR7738643_bin.71_genomic.fna/markers.fasta)
[2023-06-04 21:25:27,955] [INFO] Task started: Blastn
[2023-06-04 21:25:27,955] [INFO] Running command: blastn -query GCA_934561065.1_ERR7738643_bin.71_genomic.fna/markers.fasta -db /var/lib/cwl/stg05c5edeb-81fe-4df9-accb-cacf6a3ed5c8/dqc_reference/reference_markers_gtdb.fasta -out GCA_934561065.1_ERR7738643_bin.71_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:25:28,900] [INFO] Task succeeded: Blastn
[2023-06-04 21:25:28,909] [INFO] Selected 10 target genomes.
[2023-06-04 21:25:28,910] [INFO] Target genome list was writen to GCA_934561065.1_ERR7738643_bin.71_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:25:28,917] [INFO] Task started: fastANI
[2023-06-04 21:25:28,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a719137-e32d-478b-8684-bbbb93f25aa3/GCA_934561065.1_ERR7738643_bin.71_genomic.fna.gz --refList GCA_934561065.1_ERR7738643_bin.71_genomic.fna/target_genomes_gtdb.txt --output GCA_934561065.1_ERR7738643_bin.71_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:25:33,100] [INFO] Task succeeded: fastANI
[2023-06-04 21:25:33,113] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 21:25:33,114] [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_900548615.1	s__CAG-83 sp900548615	87.0424	337	499	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.93	97.80	0.81	0.77	3	-
GCA_900552725.1	s__CAG-83 sp900552725	86.8862	333	499	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.50	98.05	0.78	0.74	4	-
GCA_900555735.1	s__CAG-83 sp900555735	85.7178	284	499	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.84	99.67	0.89	0.81	3	-
GCA_900757415.1	s__CAG-83 sp900757415	83.0256	221	499	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.36	98.36	0.67	0.67	2	-
GCA_003487665.1	s__CAG-83 sp003487665	81.5351	253	499	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_900551355.1	s__CAG-83 sp900551355	81.5328	218	499	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	81.3321	248	499	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	81.2536	258	499	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	80.9349	264	499	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_900317425.1	s__CAG-83 sp900317425	80.8032	200	499	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.98	99.98	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-04 21:25:33,118] [INFO] GTDB search result was written to GCA_934561065.1_ERR7738643_bin.71_genomic.fna/result_gtdb.tsv
[2023-06-04 21:25:33,119] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:25:33,145] [INFO] DFAST_QC result json was written to GCA_934561065.1_ERR7738643_bin.71_genomic.fna/dqc_result.json
[2023-06-04 21:25:33,146] [INFO] DFAST_QC completed!
[2023-06-04 21:25:33,146] [INFO] Total running time: 0h0m40s