[2023-06-29 21:41:51,515] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:41:51,518] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:41:51,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg842d5b49-61b1-453f-bf8e-bac1f83c83b1/dqc_reference
[2023-06-29 21:41:52,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:41:52,938] [INFO] Task started: Prodigal
[2023-06-29 21:41:52,938] [INFO] Running command: gunzip -c /var/lib/cwl/stgda38920c-7c36-4e98-b481-a2e38ae0ff3c/GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna.gz | prodigal -d GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/cds.fna -a GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:42:08,803] [INFO] Task succeeded: Prodigal
[2023-06-29 21:42:08,804] [INFO] Task started: HMMsearch
[2023-06-29 21:42:08,804] [INFO] Running command: hmmsearch --tblout GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg842d5b49-61b1-453f-bf8e-bac1f83c83b1/dqc_reference/reference_markers.hmm GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:42:09,060] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:42:09,061] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgda38920c-7c36-4e98-b481-a2e38ae0ff3c/GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna.gz]
[2023-06-29 21:42:09,093] [INFO] Query marker FASTA was written to GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/markers.fasta
[2023-06-29 21:42:09,094] [INFO] Task started: Blastn
[2023-06-29 21:42:09,094] [INFO] Running command: blastn -query GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/markers.fasta -db /var/lib/cwl/stg842d5b49-61b1-453f-bf8e-bac1f83c83b1/dqc_reference/reference_markers.fasta -out GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:42:09,646] [INFO] Task succeeded: Blastn
[2023-06-29 21:42:09,650] [INFO] Selected 10 target genomes.
[2023-06-29 21:42:09,651] [INFO] Target genome list was writen to GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/target_genomes.txt
[2023-06-29 21:42:09,721] [INFO] Task started: fastANI
[2023-06-29 21:42:09,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgda38920c-7c36-4e98-b481-a2e38ae0ff3c/GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna.gz --refList GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/target_genomes.txt --output GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:42:17,653] [INFO] Task succeeded: fastANI
[2023-06-29 21:42:17,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg842d5b49-61b1-453f-bf8e-bac1f83c83b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:42:17,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg842d5b49-61b1-453f-bf8e-bac1f83c83b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:42:17,659] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:42:17,659] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:42:17,660] [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
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	76.144	57	703	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	76.0706	73	703	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	76.0041	51	703	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:42:17,662] [INFO] DFAST Taxonomy check result was written to GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/tc_result.tsv
[2023-06-29 21:42:17,663] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:42:17,663] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:42:17,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg842d5b49-61b1-453f-bf8e-bac1f83c83b1/dqc_reference/checkm_data
[2023-06-29 21:42:17,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:42:17,700] [INFO] Task started: CheckM
[2023-06-29 21:42:17,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/checkm_input GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/checkm_result
[2023-06-29 21:43:01,422] [INFO] Task succeeded: CheckM
[2023-06-29 21:43:01,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:43:01,446] [INFO] ===== Completeness check finished =====
[2023-06-29 21:43:01,446] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:43:01,446] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/markers.fasta)
[2023-06-29 21:43:01,447] [INFO] Task started: Blastn
[2023-06-29 21:43:01,447] [INFO] Running command: blastn -query GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/markers.fasta -db /var/lib/cwl/stg842d5b49-61b1-453f-bf8e-bac1f83c83b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:43:02,448] [INFO] Task succeeded: Blastn
[2023-06-29 21:43:02,465] [INFO] Selected 15 target genomes.
[2023-06-29 21:43:02,465] [INFO] Target genome list was writen to GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:43:02,491] [INFO] Task started: fastANI
[2023-06-29 21:43:02,491] [INFO] Running command: fastANI --query /var/lib/cwl/stgda38920c-7c36-4e98-b481-a2e38ae0ff3c/GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna.gz --refList GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/target_genomes_gtdb.txt --output GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:43:11,750] [INFO] Task succeeded: fastANI
[2023-06-29 21:43:11,765] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 21:43:11,765] [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_003151515.1	s__Palsa-1447 sp003151515	77.3891	103	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903890485.1	s__Palsa-1447 sp903890485	77.2611	116	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	99.79	99.69	0.94	0.93	6	-
GCA_903830425.1	s__Opi-474 sp903830425	77.2234	121	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.49	99.28	0.91	0.87	25	-
GCA_903872505.1	s__Opi-474 sp903872505	77.1185	123	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.99	99.98	0.99	0.99	3	-
GCA_018239845.1	s__Opitutus sp018239845	77.1073	122	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887455.1	s__Palsa-1447 sp903887455	77.0998	111	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	99.90	99.90	0.83	0.83	2	-
GCA_003164715.1	s__Palsa-1447 sp003164715	77.0954	114	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003168315.1	s__Palsa-1447 sp003168315	76.9689	86	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903827245.1	s__CAIUWA01 sp903827245	76.9177	104	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIUWA01	95.0	99.70	98.73	0.93	0.80	13	-
GCA_018239675.1	s__Opi-474 sp018239675	76.9072	120	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525695.1	s__ER46 sp011525695	76.252	76	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054705.1	s__ER46 sp003054705	76.2436	99	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019965.1	s__Opitutus terrae	76.0933	72	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903896015.1	s__CAITWF01 sp903896015	76.0053	73	703	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	99.72	99.39	0.95	0.93	8	-
--------------------------------------------------------------------------------
[2023-06-29 21:43:11,767] [INFO] GTDB search result was written to GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/result_gtdb.tsv
[2023-06-29 21:43:11,768] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:43:11,771] [INFO] DFAST_QC result json was written to GCA_903883165.1_freshwater_MAG_---_B4coas_bin-1100_genomic.fna/dqc_result.json
[2023-06-29 21:43:11,771] [INFO] DFAST_QC completed!
[2023-06-29 21:43:11,771] [INFO] Total running time: 0h1m20s