[2023-06-29 21:28:34,593] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:28:34,596] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:28:34,596] [INFO] DQC Reference Directory: /var/lib/cwl/stgf718844f-edb0-46d6-b0ba-38c8dda31887/dqc_reference
[2023-06-29 21:28:35,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:28:35,780] [INFO] Task started: Prodigal
[2023-06-29 21:28:35,781] [INFO] Running command: gunzip -c /var/lib/cwl/stgab7d505b-7d30-4568-beee-ac06cf7fa746/GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna.gz | prodigal -d GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/cds.fna -a GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:28:41,165] [INFO] Task succeeded: Prodigal
[2023-06-29 21:28:41,166] [INFO] Task started: HMMsearch
[2023-06-29 21:28:41,166] [INFO] Running command: hmmsearch --tblout GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf718844f-edb0-46d6-b0ba-38c8dda31887/dqc_reference/reference_markers.hmm GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:28:41,332] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:28:41,333] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgab7d505b-7d30-4568-beee-ac06cf7fa746/GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna.gz]
[2023-06-29 21:28:41,358] [INFO] Query marker FASTA was written to GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/markers.fasta
[2023-06-29 21:28:41,358] [INFO] Task started: Blastn
[2023-06-29 21:28:41,358] [INFO] Running command: blastn -query GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/markers.fasta -db /var/lib/cwl/stgf718844f-edb0-46d6-b0ba-38c8dda31887/dqc_reference/reference_markers.fasta -out GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:28:42,133] [INFO] Task succeeded: Blastn
[2023-06-29 21:28:42,137] [INFO] Selected 26 target genomes.
[2023-06-29 21:28:42,137] [INFO] Target genome list was writen to GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/target_genomes.txt
[2023-06-29 21:28:42,141] [INFO] Task started: fastANI
[2023-06-29 21:28:42,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgab7d505b-7d30-4568-beee-ac06cf7fa746/GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna.gz --refList GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/target_genomes.txt --output GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:29:00,683] [INFO] Task succeeded: fastANI
[2023-06-29 21:29:00,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf718844f-edb0-46d6-b0ba-38c8dda31887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:29:00,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf718844f-edb0-46d6-b0ba-38c8dda31887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:29:00,697] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:29:00,697] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:29:00,697] [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
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	76.153	111	495	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.7983	109	495	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	75.6765	124	495	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	75.6538	88	495	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	75.5359	125	495	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	75.5353	74	495	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	75.4982	131	495	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	75.3613	103	495	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	75.3504	129	495	95	below_threshold
Actinosynnema mirum	strain=DSM 43827	GCA_000023245.1	40567	40567	type	True	75.17	79	495	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	75.1491	75	495	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	75.123	85	495	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	75.108	53	495	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	75.0916	54	495	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	75.0834	76	495	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	75.0639	56	495	95	below_threshold
Amycolatopsis xylanica	strain=CPCC 202699	GCA_900107045.1	589385	589385	type	True	74.9388	69	495	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:29:00,699] [INFO] DFAST Taxonomy check result was written to GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/tc_result.tsv
[2023-06-29 21:29:00,699] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:29:00,700] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:29:00,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf718844f-edb0-46d6-b0ba-38c8dda31887/dqc_reference/checkm_data
[2023-06-29 21:29:00,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:29:00,725] [INFO] Task started: CheckM
[2023-06-29 21:29:00,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/checkm_input GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/checkm_result
[2023-06-29 21:29:22,634] [INFO] Task succeeded: CheckM
[2023-06-29 21:29:22,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.26%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 21:29:22,688] [INFO] ===== Completeness check finished =====
[2023-06-29 21:29:22,688] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:29:22,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/markers.fasta)
[2023-06-29 21:29:22,689] [INFO] Task started: Blastn
[2023-06-29 21:29:22,689] [INFO] Running command: blastn -query GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/markers.fasta -db /var/lib/cwl/stgf718844f-edb0-46d6-b0ba-38c8dda31887/dqc_reference/reference_markers_gtdb.fasta -out GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:29:24,017] [INFO] Task succeeded: Blastn
[2023-06-29 21:29:24,021] [INFO] Selected 7 target genomes.
[2023-06-29 21:29:24,021] [INFO] Target genome list was writen to GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:29:24,024] [INFO] Task started: fastANI
[2023-06-29 21:29:24,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgab7d505b-7d30-4568-beee-ac06cf7fa746/GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna.gz --refList GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/target_genomes_gtdb.txt --output GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:29:27,120] [INFO] Task succeeded: fastANI
[2023-06-29 21:29:27,128] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:29:27,128] [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_903847495.1	s__F1-60-MAGs149 sp903847495	100.0	483	495	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903960645.1	s__F1-60-MAGs149 sp903960645	85.1108	318	495	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	98.37	98.10	0.78	0.76	11	-
GCA_903873565.1	s__F1-60-MAGs149 sp903873565	81.6708	274	495	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	98.96	98.77	0.82	0.80	5	-
GCA_016870485.1	s__F1-60-MAGs149 sp016870485	81.3924	330	495	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462095.1	s__F1-60-MAGs149 sp016462095	79.6451	214	495	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694475.1	s__F1-60-MAGs149 sp009694475	79.1271	200	495	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005798855.1	s__F1-60-MAGs149 sp005798855	78.8148	211	495	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	99.87	99.85	0.93	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-29 21:29:27,130] [INFO] GTDB search result was written to GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/result_gtdb.tsv
[2023-06-29 21:29:27,131] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:29:27,134] [INFO] DFAST_QC result json was written to GCA_903847495.1_freshwater_MAG_---_Loclat_bin-15560_genomic.fna/dqc_result.json
[2023-06-29 21:29:27,135] [INFO] DFAST_QC completed!
[2023-06-29 21:29:27,135] [INFO] Total running time: 0h0m53s