[2024-01-25 17:50:05,661] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:05,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:05,662] [INFO] DQC Reference Directory: /var/lib/cwl/stg687f7cba-8fa6-4365-9bea-4a4a5beb2369/dqc_reference
[2024-01-25 17:50:06,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:06,805] [INFO] Task started: Prodigal
[2024-01-25 17:50:06,805] [INFO] Running command: gunzip -c /var/lib/cwl/stg47ddafea-5c76-42f5-9e85-f7d02cee94c7/GCF_000429365.1_ASM42936v1_genomic.fna.gz | prodigal -d GCF_000429365.1_ASM42936v1_genomic.fna/cds.fna -a GCF_000429365.1_ASM42936v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:19,069] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:19,069] [INFO] Task started: HMMsearch
[2024-01-25 17:50:19,069] [INFO] Running command: hmmsearch --tblout GCF_000429365.1_ASM42936v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg687f7cba-8fa6-4365-9bea-4a4a5beb2369/dqc_reference/reference_markers.hmm GCF_000429365.1_ASM42936v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:19,395] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:19,396] [INFO] Found 6/6 markers.
[2024-01-25 17:50:19,438] [INFO] Query marker FASTA was written to GCF_000429365.1_ASM42936v1_genomic.fna/markers.fasta
[2024-01-25 17:50:19,438] [INFO] Task started: Blastn
[2024-01-25 17:50:19,438] [INFO] Running command: blastn -query GCF_000429365.1_ASM42936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg687f7cba-8fa6-4365-9bea-4a4a5beb2369/dqc_reference/reference_markers.fasta -out GCF_000429365.1_ASM42936v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:20,297] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:20,300] [INFO] Selected 20 target genomes.
[2024-01-25 17:50:20,301] [INFO] Target genome list was writen to GCF_000429365.1_ASM42936v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:20,310] [INFO] Task started: fastANI
[2024-01-25 17:50:20,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg47ddafea-5c76-42f5-9e85-f7d02cee94c7/GCF_000429365.1_ASM42936v1_genomic.fna.gz --refList GCF_000429365.1_ASM42936v1_genomic.fna/target_genomes.txt --output GCF_000429365.1_ASM42936v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:50:37,448] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:37,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg687f7cba-8fa6-4365-9bea-4a4a5beb2369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:50:37,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg687f7cba-8fa6-4365-9bea-4a4a5beb2369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:50:37,462] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:50:37,463] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:50:37,463] [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
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	100.0	1527	1531	95	conclusive
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	99.973	1503	1531	95	conclusive
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	81.8601	843	1531	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	80.5459	764	1531	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	79.4513	673	1531	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.2483	539	1531	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.1835	555	1531	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.135	562	1531	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.1092	520	1531	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.992	560	1531	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.8848	569	1531	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.8609	561	1531	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.6115	556	1531	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.3741	511	1531	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.0733	436	1531	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.7951	351	1531	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.7703	336	1531	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.7605	337	1531	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7242	368	1531	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.2606	301	1531	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:50:37,465] [INFO] DFAST Taxonomy check result was written to GCF_000429365.1_ASM42936v1_genomic.fna/tc_result.tsv
[2024-01-25 17:50:37,466] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:50:37,466] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:50:37,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg687f7cba-8fa6-4365-9bea-4a4a5beb2369/dqc_reference/checkm_data
[2024-01-25 17:50:37,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:50:37,513] [INFO] Task started: CheckM
[2024-01-25 17:50:37,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429365.1_ASM42936v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429365.1_ASM42936v1_genomic.fna/checkm_input GCF_000429365.1_ASM42936v1_genomic.fna/checkm_result
[2024-01-25 17:51:15,548] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:15,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:15,565] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:15,565] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:15,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429365.1_ASM42936v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:15,566] [INFO] Task started: Blastn
[2024-01-25 17:51:15,566] [INFO] Running command: blastn -query GCF_000429365.1_ASM42936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg687f7cba-8fa6-4365-9bea-4a4a5beb2369/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429365.1_ASM42936v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:17,009] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:17,012] [INFO] Selected 21 target genomes.
[2024-01-25 17:51:17,012] [INFO] Target genome list was writen to GCF_000429365.1_ASM42936v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:17,028] [INFO] Task started: fastANI
[2024-01-25 17:51:17,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg47ddafea-5c76-42f5-9e85-f7d02cee94c7/GCF_000429365.1_ASM42936v1_genomic.fna.gz --refList GCF_000429365.1_ASM42936v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429365.1_ASM42936v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:38,378] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:38,391] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:38,391] [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
GCF_000429365.1	s__Pseudodonghicola xiamenensis	100.0	1527	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	conclusive
GCF_004358185.1	s__Antarcticimicrobium luteum	81.8656	842	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	80.5674	762	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	79.4986	669	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	79.4596	670	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_900129345.1	s__Ruegeria intermedia	79.2483	539	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.1585	558	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	79.1039	660	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	79.102	521	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	79.0213	533	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001458395.1	s__Leisingera aquaemixtae	78.8813	569	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_013031405.1	s__Ruegeria sp013031405	78.874	561	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	78.8611	561	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCA_006226775.1	s__Marinovum sp006226775	78.8515	516	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.7586	527	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	78.6694	592	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_013032855.1	s__Ruegeria arenilitoris	78.6661	473	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCA_018401465.1	s__Aestuariivita sp018401465	78.2976	495	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	77.9218	350	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	77.7951	351	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363615.1	s__Ruegeria sp009363615	77.7887	362	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.20	96.03	0.88	0.85	16	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:38,403] [INFO] GTDB search result was written to GCF_000429365.1_ASM42936v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:38,403] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:38,407] [INFO] DFAST_QC result json was written to GCF_000429365.1_ASM42936v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:38,407] [INFO] DFAST_QC completed!
[2024-01-25 17:51:38,407] [INFO] Total running time: 0h1m33s