[2023-06-17 06:59:57,022] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:59:57,027] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:59:57,027] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e528902-9f74-4a1c-b3c4-cce45d9e3ad5/dqc_reference
[2023-06-17 06:59:58,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:59:58,285] [INFO] Task started: Prodigal
[2023-06-17 06:59:58,286] [INFO] Running command: gunzip -c /var/lib/cwl/stg791c0eb7-b750-427e-a3b9-8d4d7ad55f11/GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna.gz | prodigal -d GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/cds.fna -a GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:00:02,998] [INFO] Task succeeded: Prodigal
[2023-06-17 07:00:02,998] [INFO] Task started: HMMsearch
[2023-06-17 07:00:02,998] [INFO] Running command: hmmsearch --tblout GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e528902-9f74-4a1c-b3c4-cce45d9e3ad5/dqc_reference/reference_markers.hmm GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:00:03,214] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:00:03,215] [INFO] Found 6/6 markers.
[2023-06-17 07:00:03,242] [INFO] Query marker FASTA was written to GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/markers.fasta
[2023-06-17 07:00:03,242] [INFO] Task started: Blastn
[2023-06-17 07:00:03,242] [INFO] Running command: blastn -query GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e528902-9f74-4a1c-b3c4-cce45d9e3ad5/dqc_reference/reference_markers.fasta -out GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:00:03,822] [INFO] Task succeeded: Blastn
[2023-06-17 07:00:03,827] [INFO] Selected 23 target genomes.
[2023-06-17 07:00:03,828] [INFO] Target genome list was writen to GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/target_genomes.txt
[2023-06-17 07:00:03,838] [INFO] Task started: fastANI
[2023-06-17 07:00:03,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg791c0eb7-b750-427e-a3b9-8d4d7ad55f11/GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna.gz --refList GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/target_genomes.txt --output GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 07:00:17,629] [INFO] Task succeeded: fastANI
[2023-06-17 07:00:17,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e528902-9f74-4a1c-b3c4-cce45d9e3ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 07:00:17,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e528902-9f74-4a1c-b3c4-cce45d9e3ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 07:00:17,631] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 07:00:17,632] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 07:00:17,632] [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
--------------------------------------------------------------------------------
[2023-06-17 07:00:17,634] [INFO] DFAST Taxonomy check result was written to GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/tc_result.tsv
[2023-06-17 07:00:17,634] [INFO] ===== Taxonomy check completed =====
[2023-06-17 07:00:17,635] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:00:17,635] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e528902-9f74-4a1c-b3c4-cce45d9e3ad5/dqc_reference/checkm_data
[2023-06-17 07:00:17,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:00:17,660] [INFO] Task started: CheckM
[2023-06-17 07:00:17,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/checkm_input GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/checkm_result
[2023-06-17 07:00:38,834] [INFO] Task succeeded: CheckM
[2023-06-17 07:00:38,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 07:00:38,860] [INFO] ===== Completeness check finished =====
[2023-06-17 07:00:38,861] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:00:38,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/markers.fasta)
[2023-06-17 07:00:38,861] [INFO] Task started: Blastn
[2023-06-17 07:00:38,861] [INFO] Running command: blastn -query GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e528902-9f74-4a1c-b3c4-cce45d9e3ad5/dqc_reference/reference_markers_gtdb.fasta -out GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:00:39,671] [INFO] Task succeeded: Blastn
[2023-06-17 07:00:39,674] [INFO] Selected 13 target genomes.
[2023-06-17 07:00:39,675] [INFO] Target genome list was writen to GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:00:39,682] [INFO] Task started: fastANI
[2023-06-17 07:00:39,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg791c0eb7-b750-427e-a3b9-8d4d7ad55f11/GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna.gz --refList GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/target_genomes_gtdb.txt --output GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:00:44,180] [INFO] Task succeeded: fastANI
[2023-06-17 07:00:44,188] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:00:44,188] [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_900542065.1	s__CAG-1427 sp000431675	99.9773	587	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	99.98	99.97	0.99	0.98	3	conclusive
GCA_900551155.1	s__CAG-1427 sp900551155	93.8905	397	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	98.93	98.93	0.80	0.80	2	-
GCA_900548955.1	s__CAG-1427 sp900548955	89.0788	381	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	99.92	99.92	0.92	0.92	2	-
GCA_000435475.1	s__CAG-1427 sp000435475	81.5278	306	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	96.89	96.41	0.87	0.87	4	-
GCA_900556585.1	s__CAG-1427 sp900556585	80.3278	171	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	98.47	98.45	0.84	0.83	3	-
GCA_900554685.1	s__CAG-1427 sp900554685	78.9093	223	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	99.84	99.84	0.88	0.88	2	-
GCA_900539675.1	s__CAG-1427 sp900539675	78.7294	147	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547965.1	s__CAG-1427 sp900547965	78.4962	93	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	99.87	99.87	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-17 07:00:44,190] [INFO] GTDB search result was written to GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/result_gtdb.tsv
[2023-06-17 07:00:44,190] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:00:44,193] [INFO] DFAST_QC result json was written to GCA_905187795.1_ERR414369-mag-bin.5_genomic.fna/dqc_result.json
[2023-06-17 07:00:44,193] [INFO] DFAST_QC completed!
[2023-06-17 07:00:44,193] [INFO] Total running time: 0h0m47s