[2023-06-28 21:02:06,623] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:02:06,625] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:02:06,625] [INFO] DQC Reference Directory: /var/lib/cwl/stge4eaec7a-f611-4516-8756-9d13246c5630/dqc_reference
[2023-06-28 21:02:08,451] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:02:08,452] [INFO] Task started: Prodigal
[2023-06-28 21:02:08,453] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdee944a-82de-4ce7-8abf-8cb8d10f094e/GCA_017501495.1_ASM1750149v1_genomic.fna.gz | prodigal -d GCA_017501495.1_ASM1750149v1_genomic.fna/cds.fna -a GCA_017501495.1_ASM1750149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:02:22,420] [INFO] Task succeeded: Prodigal
[2023-06-28 21:02:22,421] [INFO] Task started: HMMsearch
[2023-06-28 21:02:22,421] [INFO] Running command: hmmsearch --tblout GCA_017501495.1_ASM1750149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4eaec7a-f611-4516-8756-9d13246c5630/dqc_reference/reference_markers.hmm GCA_017501495.1_ASM1750149v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:02:22,694] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:02:22,696] [INFO] Found 6/6 markers.
[2023-06-28 21:02:22,723] [INFO] Query marker FASTA was written to GCA_017501495.1_ASM1750149v1_genomic.fna/markers.fasta
[2023-06-28 21:02:22,724] [INFO] Task started: Blastn
[2023-06-28 21:02:22,724] [INFO] Running command: blastn -query GCA_017501495.1_ASM1750149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4eaec7a-f611-4516-8756-9d13246c5630/dqc_reference/reference_markers.fasta -out GCA_017501495.1_ASM1750149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:02:23,380] [INFO] Task succeeded: Blastn
[2023-06-28 21:02:23,386] [INFO] Selected 35 target genomes.
[2023-06-28 21:02:23,387] [INFO] Target genome list was writen to GCA_017501495.1_ASM1750149v1_genomic.fna/target_genomes.txt
[2023-06-28 21:02:23,392] [INFO] Task started: fastANI
[2023-06-28 21:02:23,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdee944a-82de-4ce7-8abf-8cb8d10f094e/GCA_017501495.1_ASM1750149v1_genomic.fna.gz --refList GCA_017501495.1_ASM1750149v1_genomic.fna/target_genomes.txt --output GCA_017501495.1_ASM1750149v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:02:46,322] [INFO] Task succeeded: fastANI
[2023-06-28 21:02:46,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4eaec7a-f611-4516-8756-9d13246c5630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:02:46,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4eaec7a-f611-4516-8756-9d13246c5630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:02:46,326] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:02:46,326] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:02:46,326] [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
--------------------------------------------------------------------------------
[2023-06-28 21:02:46,328] [INFO] DFAST Taxonomy check result was written to GCA_017501495.1_ASM1750149v1_genomic.fna/tc_result.tsv
[2023-06-28 21:02:46,329] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:02:46,329] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:02:46,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4eaec7a-f611-4516-8756-9d13246c5630/dqc_reference/checkm_data
[2023-06-28 21:02:46,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:02:46,359] [INFO] Task started: CheckM
[2023-06-28 21:02:46,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017501495.1_ASM1750149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017501495.1_ASM1750149v1_genomic.fna/checkm_input GCA_017501495.1_ASM1750149v1_genomic.fna/checkm_result
[2023-06-28 21:03:27,750] [INFO] Task succeeded: CheckM
[2023-06-28 21:03:27,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:03:27,777] [INFO] ===== Completeness check finished =====
[2023-06-28 21:03:27,778] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:03:27,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017501495.1_ASM1750149v1_genomic.fna/markers.fasta)
[2023-06-28 21:03:27,779] [INFO] Task started: Blastn
[2023-06-28 21:03:27,779] [INFO] Running command: blastn -query GCA_017501495.1_ASM1750149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4eaec7a-f611-4516-8756-9d13246c5630/dqc_reference/reference_markers_gtdb.fasta -out GCA_017501495.1_ASM1750149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:03:28,737] [INFO] Task succeeded: Blastn
[2023-06-28 21:03:28,742] [INFO] Selected 24 target genomes.
[2023-06-28 21:03:28,742] [INFO] Target genome list was writen to GCA_017501495.1_ASM1750149v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:03:28,757] [INFO] Task started: fastANI
[2023-06-28 21:03:28,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdee944a-82de-4ce7-8abf-8cb8d10f094e/GCA_017501495.1_ASM1750149v1_genomic.fna.gz --refList GCA_017501495.1_ASM1750149v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017501495.1_ASM1750149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:03:39,841] [INFO] Task succeeded: fastANI
[2023-06-28 21:03:39,861] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:03:39,861] [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_017501495.1	s__UBA1711 sp017501495	100.0	655	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017522105.1	s__UBA1711 sp017522105	82.5387	357	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314925.1	s__UBA1711 sp900314925	82.5129	373	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.65	96.66	0.91	0.86	9	-
GCA_002372855.1	s__UBA1711 sp002372855	82.3259	297	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.33	96.12	0.84	0.73	7	-
GCA_017480785.1	s__UBA1711 sp017480785	81.3408	310	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483575.1	s__UBA1711 sp017483575	81.3032	282	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775135.1	s__UBA1711 sp902775135	81.1508	322	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784865.1	s__UBA1711 sp902784865	81.1131	324	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.01	98.97	0.93	0.93	3	-
GCA_902778925.1	s__UBA1711 sp902778925	81.0822	351	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.18	98.06	0.86	0.82	3	-
GCA_900318275.1	s__UBA1711 sp900318275	81.0757	338	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.21	97.13	0.91	0.87	7	-
GCA_902774395.1	s__UBA1711 sp902774395	80.8119	298	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002349055.1	s__UBA1711 sp002349055	80.7287	320	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.90	99.90	0.97	0.97	2	-
GCA_902791695.1	s__UBA1711 sp902791695	80.6938	292	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320975.1	s__UBA1711 sp900320975	80.3603	278	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.10	98.20	0.97	0.96	3	-
GCA_900315935.1	s__UBA1711 sp900315935	80.3326	317	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.03	97.38	0.90	0.84	6	-
GCA_900317285.1	s__UBA1711 sp900317285	80.2968	276	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.22	97.84	0.89	0.83	21	-
GCA_017524785.1	s__UBA1711 sp017524785	80.1806	285	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017542345.1	s__UBA1711 sp017542345	80.1262	188	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017940465.1	s__UBA1711 sp017940465	80.0236	289	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782185.1	s__UBA1711 sp902782185	79.8577	275	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316055.1	s__UBA1711 sp900316055	79.5073	257	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.58	97.33	0.92	0.85	5	-
GCA_017480225.1	s__UBA1711 sp017480225	79.4346	235	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017479385.1	s__UBA1711 sp017479385	77.8719	178	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:03:39,863] [INFO] GTDB search result was written to GCA_017501495.1_ASM1750149v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:03:39,863] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:03:39,867] [INFO] DFAST_QC result json was written to GCA_017501495.1_ASM1750149v1_genomic.fna/dqc_result.json
[2023-06-28 21:03:39,867] [INFO] DFAST_QC completed!
[2023-06-28 21:03:39,867] [INFO] Total running time: 0h1m33s