[2023-06-30 01:12:06,908] [INFO] DFAST_QC pipeline started.
[2023-06-30 01:12:06,912] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 01:12:06,913] [INFO] DQC Reference Directory: /var/lib/cwl/stg32848873-3e70-4991-b66e-b6b1cc09092a/dqc_reference
[2023-06-30 01:12:08,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 01:12:08,266] [INFO] Task started: Prodigal
[2023-06-30 01:12:08,266] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cc1ce79-7385-4668-9ebd-6314b9a9badb/GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna.gz | prodigal -d GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/cds.fna -a GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 01:12:11,397] [INFO] Task succeeded: Prodigal
[2023-06-30 01:12:11,397] [INFO] Task started: HMMsearch
[2023-06-30 01:12:11,397] [INFO] Running command: hmmsearch --tblout GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32848873-3e70-4991-b66e-b6b1cc09092a/dqc_reference/reference_markers.hmm GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/protein.faa > /dev/null
[2023-06-30 01:12:11,625] [INFO] Task succeeded: HMMsearch
[2023-06-30 01:12:11,626] [INFO] Found 6/6 markers.
[2023-06-30 01:12:11,676] [INFO] Query marker FASTA was written to GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/markers.fasta
[2023-06-30 01:12:11,676] [INFO] Task started: Blastn
[2023-06-30 01:12:11,676] [INFO] Running command: blastn -query GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/markers.fasta -db /var/lib/cwl/stg32848873-3e70-4991-b66e-b6b1cc09092a/dqc_reference/reference_markers.fasta -out GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:12:12,432] [INFO] Task succeeded: Blastn
[2023-06-30 01:12:12,437] [INFO] Selected 25 target genomes.
[2023-06-30 01:12:12,437] [INFO] Target genome list was writen to GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/target_genomes.txt
[2023-06-30 01:12:12,444] [INFO] Task started: fastANI
[2023-06-30 01:12:12,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cc1ce79-7385-4668-9ebd-6314b9a9badb/GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna.gz --refList GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/target_genomes.txt --output GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 01:12:26,969] [INFO] Task succeeded: fastANI
[2023-06-30 01:12:26,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32848873-3e70-4991-b66e-b6b1cc09092a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 01:12:26,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32848873-3e70-4991-b66e-b6b1cc09092a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 01:12:26,972] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 01:12:26,972] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 01:12:26,973] [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
--------------------------------------------------------------------------------
[2023-06-30 01:12:26,976] [INFO] DFAST Taxonomy check result was written to GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/tc_result.tsv
[2023-06-30 01:12:26,976] [INFO] ===== Taxonomy check completed =====
[2023-06-30 01:12:26,976] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 01:12:26,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32848873-3e70-4991-b66e-b6b1cc09092a/dqc_reference/checkm_data
[2023-06-30 01:12:26,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 01:12:27,004] [INFO] Task started: CheckM
[2023-06-30 01:12:27,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/checkm_input GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/checkm_result
[2023-06-30 01:12:44,916] [INFO] Task succeeded: CheckM
[2023-06-30 01:12:44,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 2.78%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 01:12:44,940] [INFO] ===== Completeness check finished =====
[2023-06-30 01:12:44,940] [INFO] ===== Start GTDB Search =====
[2023-06-30 01:12:44,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/markers.fasta)
[2023-06-30 01:12:44,941] [INFO] Task started: Blastn
[2023-06-30 01:12:44,941] [INFO] Running command: blastn -query GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/markers.fasta -db /var/lib/cwl/stg32848873-3e70-4991-b66e-b6b1cc09092a/dqc_reference/reference_markers_gtdb.fasta -out GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:12:45,875] [INFO] Task succeeded: Blastn
[2023-06-30 01:12:45,880] [INFO] Selected 16 target genomes.
[2023-06-30 01:12:45,880] [INFO] Target genome list was writen to GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 01:12:45,889] [INFO] Task started: fastANI
[2023-06-30 01:12:45,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cc1ce79-7385-4668-9ebd-6314b9a9badb/GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna.gz --refList GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/target_genomes_gtdb.txt --output GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 01:12:50,139] [INFO] Task succeeded: fastANI
[2023-06-30 01:12:50,151] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 01:12:50,151] [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_903921405.1	s__Planktophila sp903921405	99.0606	304	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.46	97.48	0.83	0.78	9	conclusive
GCA_007279945.1	s__Planktophila sp007279945	83.3036	254	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702525.1	s__Planktophila sp009702525	82.0658	189	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.67	99.67	0.84	0.84	2	-
GCA_009701185.1	s__Planktophila sp009701185	81.725	206	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.12	98.23	0.86	0.76	6	-
GCA_903832395.1	s__Planktophila sp903832395	79.5616	142	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.52	97.23	0.83	0.79	6	-
GCA_002284895.1	s__Planktophila sp002284895	79.0067	150	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702835.1	s__Planktophila sp009702835	78.8206	129	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.51	97.96	0.78	0.76	3	-
GCA_009699645.1	s__Planktophila sp009699645	78.4414	116	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702845.1	s__Planktophila sp009702845	78.3278	114	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918325.1	s__Planktophila sp903918325	78.2915	110	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.89	98.77	0.80	0.78	4	-
GCA_009698445.1	s__Planktophila sp009698445	78.2302	126	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.86	99.84	0.93	0.93	3	-
GCA_009705165.1	s__Planktophila sp009705165	78.0053	88	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903825015.1	s__Planktophila sp903825015	77.7317	130	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.76	99.71	0.87	0.84	4	-
GCA_903852815.1	s__Planktophila sp903852815	77.6149	116	359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.74	99.65	0.91	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-30 01:12:50,154] [INFO] GTDB search result was written to GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/result_gtdb.tsv
[2023-06-30 01:12:50,154] [INFO] ===== GTDB Search completed =====
[2023-06-30 01:12:50,157] [INFO] DFAST_QC result json was written to GCA_903856755.1_freshwater_MAG_---_Ki3-D4_bin-249_genomic.fna/dqc_result.json
[2023-06-30 01:12:50,157] [INFO] DFAST_QC completed!
[2023-06-30 01:12:50,158] [INFO] Total running time: 0h0m43s