[2023-03-16 15:26:08,855] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:26:08,855] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:26:08,855] [INFO] DQC Reference Directory: /var/lib/cwl/stga4b0d848-c81f-4ad8-a46a-a31648bf2c9f/dqc_reference
[2023-03-16 15:26:11,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:26:11,534] [INFO] Task started: Prodigal
[2023-03-16 15:26:11,535] [INFO] Running command: cat /var/lib/cwl/stg0ad6b20c-fbb3-4deb-8efa-651e40659e99/OceanDNA-b28097.fa | prodigal -d OceanDNA-b28097/cds.fna -a OceanDNA-b28097/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:26:39,372] [INFO] Task succeeded: Prodigal
[2023-03-16 15:26:39,372] [INFO] Task started: HMMsearch
[2023-03-16 15:26:39,373] [INFO] Running command: hmmsearch --tblout OceanDNA-b28097/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4b0d848-c81f-4ad8-a46a-a31648bf2c9f/dqc_reference/reference_markers.hmm OceanDNA-b28097/protein.faa > /dev/null
[2023-03-16 15:26:39,591] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:26:39,592] [INFO] Found 6/6 markers.
[2023-03-16 15:26:39,612] [INFO] Query marker FASTA was written to OceanDNA-b28097/markers.fasta
[2023-03-16 15:26:39,614] [INFO] Task started: Blastn
[2023-03-16 15:26:39,614] [INFO] Running command: blastn -query OceanDNA-b28097/markers.fasta -db /var/lib/cwl/stga4b0d848-c81f-4ad8-a46a-a31648bf2c9f/dqc_reference/reference_markers.fasta -out OceanDNA-b28097/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:40,489] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:40,489] [INFO] Selected 25 target genomes.
[2023-03-16 15:26:40,490] [INFO] Target genome list was writen to OceanDNA-b28097/target_genomes.txt
[2023-03-16 15:26:40,505] [INFO] Task started: fastANI
[2023-03-16 15:26:40,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ad6b20c-fbb3-4deb-8efa-651e40659e99/OceanDNA-b28097.fa --refList OceanDNA-b28097/target_genomes.txt --output OceanDNA-b28097/fastani_result.tsv --threads 1
[2023-03-16 15:26:55,458] [INFO] Task succeeded: fastANI
[2023-03-16 15:26:55,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4b0d848-c81f-4ad8-a46a-a31648bf2c9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:26:55,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4b0d848-c81f-4ad8-a46a-a31648bf2c9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:26:55,473] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:26:55,473] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 15:26:55,473] [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
Boseongicola aestuarii	strain=CECT 8489	GCA_900184815.1	1470561	1470561	type	True	78.1714	347	1082	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.3132	226	1082	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	77.2544	133	1082	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	77.1428	141	1082	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	77.0165	126	1082	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.9464	124	1082	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	76.8779	140	1082	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	76.8054	108	1082	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.7812	121	1082	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	76.7484	113	1082	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	76.6857	97	1082	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	76.6563	118	1082	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6221	108	1082	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	76.5403	108	1082	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.4773	104	1082	95	below_threshold
Actibacterium lipolyticum	strain=CECT 8621	GCA_900184935.1	1524263	1524263	type	True	76.4174	129	1082	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	76.4141	66	1082	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.364	103	1082	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.3503	103	1082	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.3363	102	1082	95	below_threshold
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	76.3328	103	1082	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.2812	117	1082	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.2588	115	1082	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.1391	93	1082	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.0096	71	1082	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 15:26:55,473] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28097/tc_result.tsv
[2023-03-16 15:26:55,473] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:26:55,473] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:26:55,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4b0d848-c81f-4ad8-a46a-a31648bf2c9f/dqc_reference/checkm_data
[2023-03-16 15:26:55,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:26:55,478] [INFO] Task started: CheckM
[2023-03-16 15:26:55,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28097/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28097/checkm_input OceanDNA-b28097/checkm_result
[2023-03-16 15:27:48,008] [INFO] Task succeeded: CheckM
[2023-03-16 15:27:48,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:27:48,011] [INFO] ===== Completeness check finished =====
[2023-03-16 15:27:48,011] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:27:48,011] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28097/markers.fasta)
[2023-03-16 15:27:48,011] [INFO] Task started: Blastn
[2023-03-16 15:27:48,011] [INFO] Running command: blastn -query OceanDNA-b28097/markers.fasta -db /var/lib/cwl/stga4b0d848-c81f-4ad8-a46a-a31648bf2c9f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28097/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:27:49,217] [INFO] Task succeeded: Blastn
[2023-03-16 15:27:49,218] [INFO] Selected 19 target genomes.
[2023-03-16 15:27:49,218] [INFO] Target genome list was writen to OceanDNA-b28097/target_genomes_gtdb.txt
[2023-03-16 15:27:49,657] [INFO] Task started: fastANI
[2023-03-16 15:27:49,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ad6b20c-fbb3-4deb-8efa-651e40659e99/OceanDNA-b28097.fa --refList OceanDNA-b28097/target_genomes_gtdb.txt --output OceanDNA-b28097/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:28:01,719] [INFO] Task succeeded: fastANI
[2023-03-16 15:28:01,729] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 15:28:01,730] [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_900184815.1	s__Boseongicola aestuarii	78.1714	347	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042105.1	s__Boseongicola sp013042105	77.8289	275	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.16	99.16	0.85	0.85	2	-
GCA_905479635.1	s__Boseongicola sp905479635	77.7949	181	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014075275.1	s__Boseongicola sp014075275	77.6447	203	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.87	99.87	0.99	0.99	2	-
GCA_009830125.1	s__GH1-50 sp009830125	77.3132	226	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042895.1	s__Boseongicola sp013042895	77.2923	173	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	98.28	98.28	0.61	0.61	2	-
GCF_003148765.1	s__Silicimonas algicola	77.2513	134	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	76.9778	112	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_004804335.1	s__Pelagimonas sp004804335	76.8519	134	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	76.8054	108	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.755	145	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	76.7507	147	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762635.1	s__JABURR01 sp014762635	76.6689	124	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	76.6274	114	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002504165.1	s__Pacificitalea manganoxidans	76.5403	108	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificitalea	95.0	98.03	97.97	0.89	0.82	4	-
GCF_001458175.1	s__Shimia marina	76.364	103	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_004761875.1	s__Roseovarius aestuariivivens	76.3328	103	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.2897	119	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
--------------------------------------------------------------------------------
[2023-03-16 15:28:01,730] [INFO] GTDB search result was written to OceanDNA-b28097/result_gtdb.tsv
[2023-03-16 15:28:01,730] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:28:01,732] [INFO] DFAST_QC result json was written to OceanDNA-b28097/dqc_result.json
[2023-03-16 15:28:01,732] [INFO] DFAST_QC completed!
[2023-03-16 15:28:01,732] [INFO] Total running time: 0h1m53s