[2023-06-28 23:39:24,338] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:39:24,341] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:39:24,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg855fb467-ba20-463c-9622-cef3e044355d/dqc_reference
[2023-06-28 23:39:25,730] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:39:25,731] [INFO] Task started: Prodigal
[2023-06-28 23:39:25,731] [INFO] Running command: gunzip -c /var/lib/cwl/stge5395cf2-e20e-4735-ab35-7f82b193b82e/GCA_017855415.1_ASM1785541v1_genomic.fna.gz | prodigal -d GCA_017855415.1_ASM1785541v1_genomic.fna/cds.fna -a GCA_017855415.1_ASM1785541v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:39:36,496] [INFO] Task succeeded: Prodigal
[2023-06-28 23:39:36,496] [INFO] Task started: HMMsearch
[2023-06-28 23:39:36,496] [INFO] Running command: hmmsearch --tblout GCA_017855415.1_ASM1785541v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg855fb467-ba20-463c-9622-cef3e044355d/dqc_reference/reference_markers.hmm GCA_017855415.1_ASM1785541v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:39:36,795] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:39:36,796] [INFO] Found 6/6 markers.
[2023-06-28 23:39:36,834] [INFO] Query marker FASTA was written to GCA_017855415.1_ASM1785541v1_genomic.fna/markers.fasta
[2023-06-28 23:39:36,834] [INFO] Task started: Blastn
[2023-06-28 23:39:36,835] [INFO] Running command: blastn -query GCA_017855415.1_ASM1785541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg855fb467-ba20-463c-9622-cef3e044355d/dqc_reference/reference_markers.fasta -out GCA_017855415.1_ASM1785541v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:39:37,547] [INFO] Task succeeded: Blastn
[2023-06-28 23:39:37,551] [INFO] Selected 16 target genomes.
[2023-06-28 23:39:37,552] [INFO] Target genome list was writen to GCA_017855415.1_ASM1785541v1_genomic.fna/target_genomes.txt
[2023-06-28 23:39:37,558] [INFO] Task started: fastANI
[2023-06-28 23:39:37,558] [INFO] Running command: fastANI --query /var/lib/cwl/stge5395cf2-e20e-4735-ab35-7f82b193b82e/GCA_017855415.1_ASM1785541v1_genomic.fna.gz --refList GCA_017855415.1_ASM1785541v1_genomic.fna/target_genomes.txt --output GCA_017855415.1_ASM1785541v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:40:00,419] [INFO] Task succeeded: fastANI
[2023-06-28 23:40:00,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg855fb467-ba20-463c-9622-cef3e044355d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:40:00,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg855fb467-ba20-463c-9622-cef3e044355d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:40:00,425] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:40:00,426] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:40:00,426] [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
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.6365	61	1056	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	75.5223	53	1056	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.4177	70	1056	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:40:00,428] [INFO] DFAST Taxonomy check result was written to GCA_017855415.1_ASM1785541v1_genomic.fna/tc_result.tsv
[2023-06-28 23:40:00,429] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:40:00,429] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:40:00,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg855fb467-ba20-463c-9622-cef3e044355d/dqc_reference/checkm_data
[2023-06-28 23:40:00,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:40:00,472] [INFO] Task started: CheckM
[2023-06-28 23:40:00,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017855415.1_ASM1785541v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017855415.1_ASM1785541v1_genomic.fna/checkm_input GCA_017855415.1_ASM1785541v1_genomic.fna/checkm_result
[2023-06-28 23:40:36,739] [INFO] Task succeeded: CheckM
[2023-06-28 23:40:36,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:40:36,767] [INFO] ===== Completeness check finished =====
[2023-06-28 23:40:36,767] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:40:36,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017855415.1_ASM1785541v1_genomic.fna/markers.fasta)
[2023-06-28 23:40:36,768] [INFO] Task started: Blastn
[2023-06-28 23:40:36,769] [INFO] Running command: blastn -query GCA_017855415.1_ASM1785541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg855fb467-ba20-463c-9622-cef3e044355d/dqc_reference/reference_markers_gtdb.fasta -out GCA_017855415.1_ASM1785541v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:40:37,705] [INFO] Task succeeded: Blastn
[2023-06-28 23:40:37,710] [INFO] Selected 16 target genomes.
[2023-06-28 23:40:37,710] [INFO] Target genome list was writen to GCA_017855415.1_ASM1785541v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:40:37,718] [INFO] Task started: fastANI
[2023-06-28 23:40:37,718] [INFO] Running command: fastANI --query /var/lib/cwl/stge5395cf2-e20e-4735-ab35-7f82b193b82e/GCA_017855415.1_ASM1785541v1_genomic.fna.gz --refList GCA_017855415.1_ASM1785541v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017855415.1_ASM1785541v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:40:48,233] [INFO] Task succeeded: fastANI
[2023-06-28 23:40:48,249] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:40:48,249] [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_016779265.1	s__M30B53 sp016779265	99.3318	938	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__M30B53	95.0	99.26	99.20	0.88	0.86	5	conclusive
GCA_018401745.1	s__M30B53 sp018401745	79.1455	419	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__M30B53	95.0	96.02	95.94	0.68	0.66	3	-
GCA_014192425.1	s__QWPN01 sp014192425	77.1315	147	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872925.1	s__QWPN01 sp016872925	77.0525	174	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	76.9243	134	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919035.1	s__QWPN01 sp903919035	76.8815	132	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_003670825.1	s__QWPN01 sp003670825	76.8519	95	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958265.1	s__QWPN01 sp903958265	76.8472	121	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_009924545.1	s__F1-20-MAGs016 sp009924545	76.7316	128	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671185.1	s__QWPN01 sp003671185	76.7263	134	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903951635.1	s__QWOP01 sp903951635	76.5757	141	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	99.54	99.51	0.90	0.90	3	-
GCA_903885855.1	s__QWOP01 sp903885855	76.442	159	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903949225.1	s__QWOP01 sp903949225	76.4286	108	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917235.1	s__QWPN01 sp903917235	76.361	145	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.02	96.87	0.85	0.84	3	-
GCA_003669605.1	s__QWOP01 sp003669605	76.0727	90	1056	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:40:48,251] [INFO] GTDB search result was written to GCA_017855415.1_ASM1785541v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:40:48,252] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:40:48,255] [INFO] DFAST_QC result json was written to GCA_017855415.1_ASM1785541v1_genomic.fna/dqc_result.json
[2023-06-28 23:40:48,255] [INFO] DFAST_QC completed!
[2023-06-28 23:40:48,255] [INFO] Total running time: 0h1m24s