[2023-06-18 22:56:59,318] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:56:59,320] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:56:59,320] [INFO] DQC Reference Directory: /var/lib/cwl/stg044ff844-4618-44f5-9faf-2f5279ff491f/dqc_reference
[2023-06-18 22:57:00,550] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:57:00,551] [INFO] Task started: Prodigal
[2023-06-18 22:57:00,552] [INFO] Running command: gunzip -c /var/lib/cwl/stgaeccfb6f-573c-4301-adf9-3a1588612cc0/GCA_018065615.1_ASM1806561v1_genomic.fna.gz | prodigal -d GCA_018065615.1_ASM1806561v1_genomic.fna/cds.fna -a GCA_018065615.1_ASM1806561v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:57:12,822] [INFO] Task succeeded: Prodigal
[2023-06-18 22:57:12,823] [INFO] Task started: HMMsearch
[2023-06-18 22:57:12,823] [INFO] Running command: hmmsearch --tblout GCA_018065615.1_ASM1806561v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg044ff844-4618-44f5-9faf-2f5279ff491f/dqc_reference/reference_markers.hmm GCA_018065615.1_ASM1806561v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:57:13,008] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:57:13,009] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaeccfb6f-573c-4301-adf9-3a1588612cc0/GCA_018065615.1_ASM1806561v1_genomic.fna.gz]
[2023-06-18 22:57:13,030] [INFO] Query marker FASTA was written to GCA_018065615.1_ASM1806561v1_genomic.fna/markers.fasta
[2023-06-18 22:57:13,030] [INFO] Task started: Blastn
[2023-06-18 22:57:13,030] [INFO] Running command: blastn -query GCA_018065615.1_ASM1806561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg044ff844-4618-44f5-9faf-2f5279ff491f/dqc_reference/reference_markers.fasta -out GCA_018065615.1_ASM1806561v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:57:13,605] [INFO] Task succeeded: Blastn
[2023-06-18 22:57:13,609] [INFO] Selected 24 target genomes.
[2023-06-18 22:57:13,609] [INFO] Target genome list was writen to GCA_018065615.1_ASM1806561v1_genomic.fna/target_genomes.txt
[2023-06-18 22:57:13,612] [INFO] Task started: fastANI
[2023-06-18 22:57:13,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgaeccfb6f-573c-4301-adf9-3a1588612cc0/GCA_018065615.1_ASM1806561v1_genomic.fna.gz --refList GCA_018065615.1_ASM1806561v1_genomic.fna/target_genomes.txt --output GCA_018065615.1_ASM1806561v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:57:27,074] [INFO] Task succeeded: fastANI
[2023-06-18 22:57:27,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg044ff844-4618-44f5-9faf-2f5279ff491f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:57:27,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg044ff844-4618-44f5-9faf-2f5279ff491f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:57:27,076] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:57:27,076] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 22:57:27,076] [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
--------------------------------------------------------------------------------
[2023-06-18 22:57:27,078] [INFO] DFAST Taxonomy check result was written to GCA_018065615.1_ASM1806561v1_genomic.fna/tc_result.tsv
[2023-06-18 22:57:27,078] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:57:27,078] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:57:27,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg044ff844-4618-44f5-9faf-2f5279ff491f/dqc_reference/checkm_data
[2023-06-18 22:57:27,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:57:27,104] [INFO] Task started: CheckM
[2023-06-18 22:57:27,104] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018065615.1_ASM1806561v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018065615.1_ASM1806561v1_genomic.fna/checkm_input GCA_018065615.1_ASM1806561v1_genomic.fna/checkm_result
[2023-06-18 22:58:07,040] [INFO] Task succeeded: CheckM
[2023-06-18 22:58:07,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:58:07,058] [INFO] ===== Completeness check finished =====
[2023-06-18 22:58:07,058] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:58:07,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018065615.1_ASM1806561v1_genomic.fna/markers.fasta)
[2023-06-18 22:58:07,059] [INFO] Task started: Blastn
[2023-06-18 22:58:07,059] [INFO] Running command: blastn -query GCA_018065615.1_ASM1806561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg044ff844-4618-44f5-9faf-2f5279ff491f/dqc_reference/reference_markers_gtdb.fasta -out GCA_018065615.1_ASM1806561v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:58:07,826] [INFO] Task succeeded: Blastn
[2023-06-18 22:58:07,830] [INFO] Selected 20 target genomes.
[2023-06-18 22:58:07,830] [INFO] Target genome list was writen to GCA_018065615.1_ASM1806561v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:58:07,841] [INFO] Task started: fastANI
[2023-06-18 22:58:07,841] [INFO] Running command: fastANI --query /var/lib/cwl/stgaeccfb6f-573c-4301-adf9-3a1588612cc0/GCA_018065615.1_ASM1806561v1_genomic.fna.gz --refList GCA_018065615.1_ASM1806561v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018065615.1_ASM1806561v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:58:16,528] [INFO] Task succeeded: fastANI
[2023-06-18 22:58:16,543] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:58:16,544] [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_018065615.1	s__UBA1179 sp018065615	100.0	682	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900319225.1	s__UBA1179 sp900319225	79.1477	258	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	98.54	97.96	0.93	0.90	5	-
GCA_017557635.1	s__UBA1179 sp017557635	79.1409	279	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.04	96.04	0.85	0.85	2	-
GCA_017530735.1	s__UBA1179 sp017530735	79.0316	247	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	98.35	98.35	0.83	0.83	2	-
GCA_900318995.1	s__UBA1179 sp900318995	78.9624	248	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.89	96.18	0.89	0.85	8	-
GCA_902798685.1	s__UBA1179 sp902798685	78.9605	258	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551925.1	s__UBA1179 sp017551925	78.8545	266	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642425.1	s__UBA1179 sp017642425	78.8054	236	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234745.1	s__UBA1179 sp905234745	78.7964	256	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779875.1	s__UBA1179 sp902779875	78.7386	247	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	98.64	98.64	0.90	0.90	2	-
GCA_902763885.1	s__UBA1179 sp902763885	78.7341	243	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799685.1	s__UBA1179 sp902799685	78.653	246	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.39	96.39	0.82	0.82	2	-
GCA_017633615.1	s__UBA1179 sp017633615	78.6425	257	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782245.1	s__UBA1179 sp902782245	78.5714	260	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.81	95.66	0.89	0.85	3	-
GCA_902774335.1	s__UBA1179 sp902774335	78.535	279	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	98.26	97.82	0.94	0.91	3	-
GCA_017551845.1	s__UBA1179 sp017551845	78.4134	174	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235565.1	s__UBA1179 sp905235565	78.4048	217	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002310015.1	s__UBA1179 sp002310015	78.2044	217	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774275.1	s__UBA1179 sp902774275	78.1598	211	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760965.1	s__UBA1179 sp902760965	78.1406	214	689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	97.44	97.44	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-18 22:58:16,546] [INFO] GTDB search result was written to GCA_018065615.1_ASM1806561v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:58:16,547] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:58:16,550] [INFO] DFAST_QC result json was written to GCA_018065615.1_ASM1806561v1_genomic.fna/dqc_result.json
[2023-06-18 22:58:16,551] [INFO] DFAST_QC completed!
[2023-06-18 22:58:16,551] [INFO] Total running time: 0h1m17s