[2023-06-27 05:57:44,123] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:57:44,131] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:57:44,131] [INFO] DQC Reference Directory: /var/lib/cwl/stgce2cfbbd-93f6-4f86-954d-c917617cb79d/dqc_reference
[2023-06-27 05:57:47,870] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:57:47,872] [INFO] Task started: Prodigal
[2023-06-27 05:57:47,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg7de4050f-befb-4d4a-a91f-47cb2f1a7b7c/GCA_026705175.1_ASM2670517v1_genomic.fna.gz | prodigal -d GCA_026705175.1_ASM2670517v1_genomic.fna/cds.fna -a GCA_026705175.1_ASM2670517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:57:59,308] [INFO] Task succeeded: Prodigal
[2023-06-27 05:57:59,309] [INFO] Task started: HMMsearch
[2023-06-27 05:57:59,309] [INFO] Running command: hmmsearch --tblout GCA_026705175.1_ASM2670517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce2cfbbd-93f6-4f86-954d-c917617cb79d/dqc_reference/reference_markers.hmm GCA_026705175.1_ASM2670517v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:57:59,569] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:57:59,570] [INFO] Found 6/6 markers.
[2023-06-27 05:57:59,613] [INFO] Query marker FASTA was written to GCA_026705175.1_ASM2670517v1_genomic.fna/markers.fasta
[2023-06-27 05:57:59,614] [INFO] Task started: Blastn
[2023-06-27 05:57:59,614] [INFO] Running command: blastn -query GCA_026705175.1_ASM2670517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce2cfbbd-93f6-4f86-954d-c917617cb79d/dqc_reference/reference_markers.fasta -out GCA_026705175.1_ASM2670517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:58:00,444] [INFO] Task succeeded: Blastn
[2023-06-27 05:58:00,448] [INFO] Selected 21 target genomes.
[2023-06-27 05:58:00,448] [INFO] Target genome list was writen to GCA_026705175.1_ASM2670517v1_genomic.fna/target_genomes.txt
[2023-06-27 05:58:00,453] [INFO] Task started: fastANI
[2023-06-27 05:58:00,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg7de4050f-befb-4d4a-a91f-47cb2f1a7b7c/GCA_026705175.1_ASM2670517v1_genomic.fna.gz --refList GCA_026705175.1_ASM2670517v1_genomic.fna/target_genomes.txt --output GCA_026705175.1_ASM2670517v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:58:15,053] [INFO] Task succeeded: fastANI
[2023-06-27 05:58:15,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce2cfbbd-93f6-4f86-954d-c917617cb79d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:58:15,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce2cfbbd-93f6-4f86-954d-c917617cb79d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:58:15,066] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:58:15,066] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 05:58:15,067] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.8647	157	1122	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.8623	160	1122	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.4345	139	1122	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.2829	105	1122	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	76.0056	55	1122	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.9453	176	1122	95	below_threshold
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	75.8997	76	1122	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	75.6692	52	1122	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	75.5414	65	1122	95	below_threshold
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	75.5052	54	1122	95	below_threshold
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	75.3865	88	1122	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	75.3355	59	1122	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	75.2234	61	1122	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:58:15,069] [INFO] DFAST Taxonomy check result was written to GCA_026705175.1_ASM2670517v1_genomic.fna/tc_result.tsv
[2023-06-27 05:58:15,069] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:58:15,069] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:58:15,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce2cfbbd-93f6-4f86-954d-c917617cb79d/dqc_reference/checkm_data
[2023-06-27 05:58:15,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:58:15,119] [INFO] Task started: CheckM
[2023-06-27 05:58:15,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026705175.1_ASM2670517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026705175.1_ASM2670517v1_genomic.fna/checkm_input GCA_026705175.1_ASM2670517v1_genomic.fna/checkm_result
[2023-06-27 05:58:56,416] [INFO] Task succeeded: CheckM
[2023-06-27 05:58:56,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:58:56,435] [INFO] ===== Completeness check finished =====
[2023-06-27 05:58:56,435] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:58:56,436] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026705175.1_ASM2670517v1_genomic.fna/markers.fasta)
[2023-06-27 05:58:56,436] [INFO] Task started: Blastn
[2023-06-27 05:58:56,436] [INFO] Running command: blastn -query GCA_026705175.1_ASM2670517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce2cfbbd-93f6-4f86-954d-c917617cb79d/dqc_reference/reference_markers_gtdb.fasta -out GCA_026705175.1_ASM2670517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:58:57,540] [INFO] Task succeeded: Blastn
[2023-06-27 05:58:57,545] [INFO] Selected 19 target genomes.
[2023-06-27 05:58:57,545] [INFO] Target genome list was writen to GCA_026705175.1_ASM2670517v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:58:57,555] [INFO] Task started: fastANI
[2023-06-27 05:58:57,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg7de4050f-befb-4d4a-a91f-47cb2f1a7b7c/GCA_026705175.1_ASM2670517v1_genomic.fna.gz --refList GCA_026705175.1_ASM2670517v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026705175.1_ASM2670517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:59:08,180] [INFO] Task succeeded: fastANI
[2023-06-27 05:59:08,208] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:59:08,209] [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_009843525.1	s__WTFX01 sp009843525	97.8133	990	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__WTFX01	95.0	98.04	97.52	0.89	0.86	18	conclusive
GCA_011523825.1	s__WTFX01 sp011523825	89.3999	882	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__WTFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009844405.1	s__VYCW01 sp009844405	77.3006	205	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.44	99.17	0.93	0.90	7	-
GCA_011051915.1	s__DRKF01 sp011051915	77.2041	106	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__DRKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882825.1	s__F1-20-MAGs160 sp018882825	77.0998	78	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969405.1	s__F1-20-MAGs160 sp018969405	77.0702	91	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	76.8623	160	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697065.1	s__J010 sp003697065	76.5575	102	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.5044	111	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_005888395.1	s__AC-25 sp005888395	76.5023	83	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-25;g__AC-25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003962875.1	s__AWTP1-35 sp003962875	76.4726	90	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719385.1	s__Microthrix sp002473265	76.4485	108	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__Microthrix	95.0	98.81	98.46	0.90	0.86	7	-
GCA_009377505.1	s__WHTX01 sp009377505	76.2804	161	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CAIXPF01;g__WHTX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268735.1	s__AWTP1-35 sp018268735	76.2272	71	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247975.1	s__JAFBAD01 sp019247975	76.1755	89	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAFBAD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888295.1	s__AC-9 sp005888295	75.9879	92	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__QHCF01;g__AC-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936035.1	s__ZC4RG19 sp016936035	75.8995	92	1122	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:59:08,211] [INFO] GTDB search result was written to GCA_026705175.1_ASM2670517v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:59:08,211] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:59:08,215] [INFO] DFAST_QC result json was written to GCA_026705175.1_ASM2670517v1_genomic.fna/dqc_result.json
[2023-06-27 05:59:08,215] [INFO] DFAST_QC completed!
[2023-06-27 05:59:08,215] [INFO] Total running time: 0h1m24s