[2023-06-13 00:24:01,264] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:24:01,266] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:24:01,266] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc65013b-2037-4450-a907-fb65d0357754/dqc_reference
[2023-06-13 00:24:02,504] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:24:02,505] [INFO] Task started: Prodigal
[2023-06-13 00:24:02,505] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6aa2575-7021-4425-94d2-e340fc62277a/GCA_022708185.1_ASM2270818v1_genomic.fna.gz | prodigal -d GCA_022708185.1_ASM2270818v1_genomic.fna/cds.fna -a GCA_022708185.1_ASM2270818v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:24:15,859] [INFO] Task succeeded: Prodigal
[2023-06-13 00:24:15,860] [INFO] Task started: HMMsearch
[2023-06-13 00:24:15,860] [INFO] Running command: hmmsearch --tblout GCA_022708185.1_ASM2270818v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc65013b-2037-4450-a907-fb65d0357754/dqc_reference/reference_markers.hmm GCA_022708185.1_ASM2270818v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:24:16,088] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:24:16,089] [INFO] Found 6/6 markers.
[2023-06-13 00:24:16,119] [INFO] Query marker FASTA was written to GCA_022708185.1_ASM2270818v1_genomic.fna/markers.fasta
[2023-06-13 00:24:16,119] [INFO] Task started: Blastn
[2023-06-13 00:24:16,119] [INFO] Running command: blastn -query GCA_022708185.1_ASM2270818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc65013b-2037-4450-a907-fb65d0357754/dqc_reference/reference_markers.fasta -out GCA_022708185.1_ASM2270818v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:24:16,663] [INFO] Task succeeded: Blastn
[2023-06-13 00:24:16,667] [INFO] Selected 20 target genomes.
[2023-06-13 00:24:16,668] [INFO] Target genome list was writen to GCA_022708185.1_ASM2270818v1_genomic.fna/target_genomes.txt
[2023-06-13 00:24:16,672] [INFO] Task started: fastANI
[2023-06-13 00:24:16,672] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6aa2575-7021-4425-94d2-e340fc62277a/GCA_022708185.1_ASM2270818v1_genomic.fna.gz --refList GCA_022708185.1_ASM2270818v1_genomic.fna/target_genomes.txt --output GCA_022708185.1_ASM2270818v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:24:30,113] [INFO] Task succeeded: fastANI
[2023-06-13 00:24:30,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc65013b-2037-4450-a907-fb65d0357754/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:24:30,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc65013b-2037-4450-a907-fb65d0357754/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:24:30,116] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:24:30,116] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 00:24:30,116] [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 00:24:30,119] [INFO] DFAST Taxonomy check result was written to GCA_022708185.1_ASM2270818v1_genomic.fna/tc_result.tsv
[2023-06-13 00:24:30,119] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:24:30,119] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:24:30,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc65013b-2037-4450-a907-fb65d0357754/dqc_reference/checkm_data
[2023-06-13 00:24:30,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:24:30,165] [INFO] Task started: CheckM
[2023-06-13 00:24:30,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708185.1_ASM2270818v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708185.1_ASM2270818v1_genomic.fna/checkm_input GCA_022708185.1_ASM2270818v1_genomic.fna/checkm_result
[2023-06-13 00:25:12,874] [INFO] Task succeeded: CheckM
[2023-06-13 00:25:12,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:25:12,895] [INFO] ===== Completeness check finished =====
[2023-06-13 00:25:12,896] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:25:12,896] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708185.1_ASM2270818v1_genomic.fna/markers.fasta)
[2023-06-13 00:25:12,896] [INFO] Task started: Blastn
[2023-06-13 00:25:12,896] [INFO] Running command: blastn -query GCA_022708185.1_ASM2270818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc65013b-2037-4450-a907-fb65d0357754/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708185.1_ASM2270818v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:25:13,637] [INFO] Task succeeded: Blastn
[2023-06-13 00:25:13,641] [INFO] Selected 26 target genomes.
[2023-06-13 00:25:13,641] [INFO] Target genome list was writen to GCA_022708185.1_ASM2270818v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:25:13,655] [INFO] Task started: fastANI
[2023-06-13 00:25:13,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6aa2575-7021-4425-94d2-e340fc62277a/GCA_022708185.1_ASM2270818v1_genomic.fna.gz --refList GCA_022708185.1_ASM2270818v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708185.1_ASM2270818v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:25:29,276] [INFO] Task succeeded: fastANI
[2023-06-13 00:25:29,289] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:25:29,290] [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_002070505.1	s__LD21 sp002070505	99.8552	997	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.69	99.69	0.88	0.88	2	conclusive
GCA_003152835.1	s__LD21 sp003152835	76.4819	98	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.43	99.38	0.90	0.89	3	-
GCA_003142255.1	s__LD21 sp003142255	76.4686	117	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.86	99.76	0.98	0.97	3	-
GCA_012517605.1	s__LD21 sp012517605	76.457	94	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.39	99.39	0.94	0.94	2	-
GCA_016715075.1	s__LD21 sp016715075	76.4563	79	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.94	98.94	0.93	0.93	2	-
GCA_003520925.1	s__LD21 sp003520925	76.1602	86	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.68	99.68	0.93	0.93	2	-
GCA_003157055.1	s__LD21 sp003157055	76.1564	67	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141415.1	s__LD21 sp003141415	76.0034	71	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003157015.1	s__LD21 sp003157015	75.9984	79	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.74	99.74	0.96	0.96	2	-
GCA_016936435.1	s__LD21 sp016936435	75.9818	84	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.88	99.88	0.95	0.95	2	-
GCA_003141525.1	s__LD21 sp003141525	75.9672	72	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.74	99.74	0.88	0.88	2	-
GCA_002328625.1	s__LD21 sp002328625	75.9631	79	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768195.1	s__LD21 sp001768195	75.9057	88	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.84	99.74	0.96	0.95	8	-
GCA_002319885.1	s__LD21 sp002319885	75.8171	78	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141495.1	s__LD21 sp003141495	75.6844	70	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003157075.1	s__LD21 sp003157075	75.2502	67	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.24	99.24	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-13 00:25:29,293] [INFO] GTDB search result was written to GCA_022708185.1_ASM2270818v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:25:29,293] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:25:29,296] [INFO] DFAST_QC result json was written to GCA_022708185.1_ASM2270818v1_genomic.fna/dqc_result.json
[2023-06-13 00:25:29,296] [INFO] DFAST_QC completed!
[2023-06-13 00:25:29,296] [INFO] Total running time: 0h1m28s