[2023-06-30 00:10:11,028] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:10:11,030] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:10:11,030] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ca791de-da2c-4d2e-b726-7c2d93f9d3db/dqc_reference
[2023-06-30 00:10:12,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:10:12,619] [INFO] Task started: Prodigal
[2023-06-30 00:10:12,619] [INFO] Running command: gunzip -c /var/lib/cwl/stgae2cf047-acb7-44f5-bca2-5fb3a232c190/GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna.gz | prodigal -d GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/cds.fna -a GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:10:20,878] [INFO] Task succeeded: Prodigal
[2023-06-30 00:10:20,878] [INFO] Task started: HMMsearch
[2023-06-30 00:10:20,879] [INFO] Running command: hmmsearch --tblout GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ca791de-da2c-4d2e-b726-7c2d93f9d3db/dqc_reference/reference_markers.hmm GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:10:21,123] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:10:21,124] [INFO] Found 6/6 markers.
[2023-06-30 00:10:21,157] [INFO] Query marker FASTA was written to GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/markers.fasta
[2023-06-30 00:10:21,157] [INFO] Task started: Blastn
[2023-06-30 00:10:21,157] [INFO] Running command: blastn -query GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ca791de-da2c-4d2e-b726-7c2d93f9d3db/dqc_reference/reference_markers.fasta -out GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:10:21,744] [INFO] Task succeeded: Blastn
[2023-06-30 00:10:21,748] [INFO] Selected 36 target genomes.
[2023-06-30 00:10:21,748] [INFO] Target genome list was writen to GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/target_genomes.txt
[2023-06-30 00:10:21,751] [INFO] Task started: fastANI
[2023-06-30 00:10:21,751] [INFO] Running command: fastANI --query /var/lib/cwl/stgae2cf047-acb7-44f5-bca2-5fb3a232c190/GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna.gz --refList GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/target_genomes.txt --output GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:10:53,864] [INFO] Task succeeded: fastANI
[2023-06-30 00:10:53,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ca791de-da2c-4d2e-b726-7c2d93f9d3db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:10:53,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ca791de-da2c-4d2e-b726-7c2d93f9d3db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:10:53,868] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:10:53,868] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:10:53,868] [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
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.8209	58	583	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:10:53,882] [INFO] DFAST Taxonomy check result was written to GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/tc_result.tsv
[2023-06-30 00:10:53,883] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:10:53,883] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:10:53,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ca791de-da2c-4d2e-b726-7c2d93f9d3db/dqc_reference/checkm_data
[2023-06-30 00:10:53,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:10:53,923] [INFO] Task started: CheckM
[2023-06-30 00:10:53,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/checkm_input GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/checkm_result
[2023-06-30 00:11:19,519] [INFO] Task succeeded: CheckM
[2023-06-30 00:11:19,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.12%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:11:19,536] [INFO] ===== Completeness check finished =====
[2023-06-30 00:11:19,536] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:11:19,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/markers.fasta)
[2023-06-30 00:11:19,536] [INFO] Task started: Blastn
[2023-06-30 00:11:19,537] [INFO] Running command: blastn -query GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ca791de-da2c-4d2e-b726-7c2d93f9d3db/dqc_reference/reference_markers_gtdb.fasta -out GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:11:20,480] [INFO] Task succeeded: Blastn
[2023-06-30 00:11:20,483] [INFO] Selected 26 target genomes.
[2023-06-30 00:11:20,483] [INFO] Target genome list was writen to GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:11:20,494] [INFO] Task started: fastANI
[2023-06-30 00:11:20,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgae2cf047-acb7-44f5-bca2-5fb3a232c190/GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna.gz --refList GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/target_genomes_gtdb.txt --output GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:11:38,625] [INFO] Task succeeded: fastANI
[2023-06-30 00:11:38,633] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:11:38,633] [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_903875225.1	s__CAIUMM01 sp903875225	76.9067	101	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAIUMM01	95.0	99.62	99.43	0.93	0.90	4	-
GCA_903959175.1	s__CAJBVW01 sp903959175	76.8477	164	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAJBVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844155.1	s__CAIUMM01 sp903844155	76.6328	87	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAIUMM01	95.0	99.98	99.97	0.97	0.97	4	-
GCA_903921785.1	s__SXON01 sp903921785	76.4093	109	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.91	0.96	0.95	4	-
GCA_014191855.1	s__SXON01 sp014191855	76.357	55	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875435.1	s__SXON01 sp016875435	76.3498	84	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903900265.1	s__CAIUMM01 sp903900265	76.2759	73	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAIUMM01	95.0	98.89	95.85	0.93	0.87	5	-
GCA_903885375.1	s__SXON01 sp903885375	76.244	98	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.89	0.96	0.95	10	-
GCA_009692585.1	s__SXON01 sp009692585	76.1565	67	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778355.1	s__SXON01 sp005778355	75.8189	100	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.89	99.88	0.95	0.94	3	-
GCA_016875315.1	s__SXON01 sp016875315	75.779	94	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226595.1	s__M1803 sp006226595	75.3552	71	583	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__M1803	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:11:38,634] [INFO] GTDB search result was written to GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/result_gtdb.tsv
[2023-06-30 00:11:38,635] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:11:38,637] [INFO] DFAST_QC result json was written to GCA_903907795.1_freshwater_MAG_---_Kiruna_bin-01303_genomic.fna/dqc_result.json
[2023-06-30 00:11:38,638] [INFO] DFAST_QC completed!
[2023-06-30 00:11:38,638] [INFO] Total running time: 0h1m28s