[2023-06-13 14:06:25,375] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:06:25,378] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:06:25,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg5da5f48e-f45c-40ea-8203-271f53adf856/dqc_reference
[2023-06-13 14:06:26,756] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:06:26,757] [INFO] Task started: Prodigal
[2023-06-13 14:06:26,757] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6eb696f-cf27-4fac-a573-e4a8150b569f/GCA_022744525.1_ASM2274452v1_genomic.fna.gz | prodigal -d GCA_022744525.1_ASM2274452v1_genomic.fna/cds.fna -a GCA_022744525.1_ASM2274452v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:06:48,654] [INFO] Task succeeded: Prodigal
[2023-06-13 14:06:48,654] [INFO] Task started: HMMsearch
[2023-06-13 14:06:48,655] [INFO] Running command: hmmsearch --tblout GCA_022744525.1_ASM2274452v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5da5f48e-f45c-40ea-8203-271f53adf856/dqc_reference/reference_markers.hmm GCA_022744525.1_ASM2274452v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:06:49,013] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:06:49,014] [INFO] Found 6/6 markers.
[2023-06-13 14:06:49,056] [INFO] Query marker FASTA was written to GCA_022744525.1_ASM2274452v1_genomic.fna/markers.fasta
[2023-06-13 14:06:49,056] [INFO] Task started: Blastn
[2023-06-13 14:06:49,057] [INFO] Running command: blastn -query GCA_022744525.1_ASM2274452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5da5f48e-f45c-40ea-8203-271f53adf856/dqc_reference/reference_markers.fasta -out GCA_022744525.1_ASM2274452v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:06:49,772] [INFO] Task succeeded: Blastn
[2023-06-13 14:06:49,776] [INFO] Selected 29 target genomes.
[2023-06-13 14:06:49,777] [INFO] Target genome list was writen to GCA_022744525.1_ASM2274452v1_genomic.fna/target_genomes.txt
[2023-06-13 14:06:49,782] [INFO] Task started: fastANI
[2023-06-13 14:06:49,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6eb696f-cf27-4fac-a573-e4a8150b569f/GCA_022744525.1_ASM2274452v1_genomic.fna.gz --refList GCA_022744525.1_ASM2274452v1_genomic.fna/target_genomes.txt --output GCA_022744525.1_ASM2274452v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:07:06,201] [INFO] Task succeeded: fastANI
[2023-06-13 14:07:06,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5da5f48e-f45c-40ea-8203-271f53adf856/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:07:06,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5da5f48e-f45c-40ea-8203-271f53adf856/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:07:06,207] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:07:06,207] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 14:07:06,207] [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
--------------------------------------------------------------------------------
[2023-06-13 14:07:06,212] [INFO] DFAST Taxonomy check result was written to GCA_022744525.1_ASM2274452v1_genomic.fna/tc_result.tsv
[2023-06-13 14:07:06,213] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:07:06,214] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:07:06,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5da5f48e-f45c-40ea-8203-271f53adf856/dqc_reference/checkm_data
[2023-06-13 14:07:06,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:07:06,280] [INFO] Task started: CheckM
[2023-06-13 14:07:06,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022744525.1_ASM2274452v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022744525.1_ASM2274452v1_genomic.fna/checkm_input GCA_022744525.1_ASM2274452v1_genomic.fna/checkm_result
[2023-06-13 14:08:08,730] [INFO] Task succeeded: CheckM
[2023-06-13 14:08:08,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:08:08,759] [INFO] ===== Completeness check finished =====
[2023-06-13 14:08:08,760] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:08:08,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022744525.1_ASM2274452v1_genomic.fna/markers.fasta)
[2023-06-13 14:08:08,760] [INFO] Task started: Blastn
[2023-06-13 14:08:08,760] [INFO] Running command: blastn -query GCA_022744525.1_ASM2274452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5da5f48e-f45c-40ea-8203-271f53adf856/dqc_reference/reference_markers_gtdb.fasta -out GCA_022744525.1_ASM2274452v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:08:09,566] [INFO] Task succeeded: Blastn
[2023-06-13 14:08:09,572] [INFO] Selected 23 target genomes.
[2023-06-13 14:08:09,572] [INFO] Target genome list was writen to GCA_022744525.1_ASM2274452v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:08:09,609] [INFO] Task started: fastANI
[2023-06-13 14:08:09,610] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6eb696f-cf27-4fac-a573-e4a8150b569f/GCA_022744525.1_ASM2274452v1_genomic.fna.gz --refList GCA_022744525.1_ASM2274452v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022744525.1_ASM2274452v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:08:18,958] [INFO] Task succeeded: fastANI
[2023-06-13 14:08:18,971] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:08:18,971] [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_000434935.1	s__Cryptobacteroides sp000434935	96.1946	667	1012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.20	96.88	0.85	0.83	4	conclusive
GCA_000432515.1	s__Cryptobacteroides sp000432515	83.0305	360	1012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.23	97.18	0.82	0.82	4	-
GCA_000435075.1	s__Cryptobacteroides sp000435075	81.4622	337	1012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.30	97.06	0.87	0.85	4	-
GCA_900546925.1	s__Cryptobacteroides sp900546925	79.7189	233	1012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.81	98.70	0.85	0.79	6	-
GCA_004552615.1	s__Cryptobacteroides sp004552615	78.5255	139	1012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.38	98.38	0.80	0.80	2	-
GCA_900769145.1	s__Cryptobacteroides sp900769145	78.4177	141	1012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004552115.1	s__Cryptobacteroides sp004552115	77.9364	118	1012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.49	98.12	0.74	0.72	3	-
GCA_016295455.1	s__Cryptobacteroides sp016295455	76.8737	52	1012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.79	98.71	0.83	0.82	3	-
GCA_017694885.1	s__Cryptobacteroides faecipullorum	76.4516	68	1012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483985.1	s__Cryptobacteroides sp017483985	76.2135	58	1012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:08:18,973] [INFO] GTDB search result was written to GCA_022744525.1_ASM2274452v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:08:18,973] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:08:18,976] [INFO] DFAST_QC result json was written to GCA_022744525.1_ASM2274452v1_genomic.fna/dqc_result.json
[2023-06-13 14:08:18,977] [INFO] DFAST_QC completed!
[2023-06-13 14:08:18,977] [INFO] Total running time: 0h1m54s