[2023-03-16 10:00:16,240] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:00:16,240] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:00:16,240] [INFO] DQC Reference Directory: /var/lib/cwl/stgda40fb41-339e-4648-a2c8-cf059f3df029/dqc_reference
[2023-03-16 10:00:17,331] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:00:17,332] [INFO] Task started: Prodigal
[2023-03-16 10:00:17,332] [INFO] Running command: cat /var/lib/cwl/stg02dd5823-603e-4f05-9d82-a23cc7da5f58/OceanDNA-b30025.fa | prodigal -d OceanDNA-b30025/cds.fna -a OceanDNA-b30025/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:00:40,895] [INFO] Task succeeded: Prodigal
[2023-03-16 10:00:40,895] [INFO] Task started: HMMsearch
[2023-03-16 10:00:40,895] [INFO] Running command: hmmsearch --tblout OceanDNA-b30025/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda40fb41-339e-4648-a2c8-cf059f3df029/dqc_reference/reference_markers.hmm OceanDNA-b30025/protein.faa > /dev/null
[2023-03-16 10:00:41,092] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:00:41,093] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg02dd5823-603e-4f05-9d82-a23cc7da5f58/OceanDNA-b30025.fa]
[2023-03-16 10:00:41,119] [INFO] Query marker FASTA was written to OceanDNA-b30025/markers.fasta
[2023-03-16 10:00:41,120] [INFO] Task started: Blastn
[2023-03-16 10:00:41,120] [INFO] Running command: blastn -query OceanDNA-b30025/markers.fasta -db /var/lib/cwl/stgda40fb41-339e-4648-a2c8-cf059f3df029/dqc_reference/reference_markers.fasta -out OceanDNA-b30025/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:00:41,691] [INFO] Task succeeded: Blastn
[2023-03-16 10:00:41,693] [INFO] Selected 25 target genomes.
[2023-03-16 10:00:41,693] [INFO] Target genome list was writen to OceanDNA-b30025/target_genomes.txt
[2023-03-16 10:00:41,701] [INFO] Task started: fastANI
[2023-03-16 10:00:41,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg02dd5823-603e-4f05-9d82-a23cc7da5f58/OceanDNA-b30025.fa --refList OceanDNA-b30025/target_genomes.txt --output OceanDNA-b30025/fastani_result.tsv --threads 1
[2023-03-16 10:00:58,129] [INFO] Task succeeded: fastANI
[2023-03-16 10:00:58,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda40fb41-339e-4648-a2c8-cf059f3df029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:00:58,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda40fb41-339e-4648-a2c8-cf059f3df029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:00:58,143] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 10:00:58,144] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 10:00:58,144] [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
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	97.6841	1111	1150	95	conclusive
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	78.1922	360	1150	95	below_threshold
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	77.8636	319	1150	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.6404	275	1150	95	below_threshold
Shimia abyssi	strain=DSM 100673	GCA_003014475.1	1662395	1662395	type	True	77.4568	230	1150	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	77.2753	223	1150	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	77.1964	227	1150	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	77.1371	229	1150	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	76.9839	138	1150	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.9177	90	1150	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	76.8974	185	1150	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	76.8885	186	1150	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.7877	180	1150	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	76.7574	173	1150	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	76.7372	171	1150	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	76.729	158	1150	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	76.7226	165	1150	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	76.668	182	1150	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	76.6611	168	1150	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	76.6549	186	1150	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	76.4356	153	1150	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.3791	120	1150	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.2368	129	1150	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	76.1082	117	1150	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.9879	91	1150	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:00:58,145] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30025/tc_result.tsv
[2023-03-16 10:00:58,145] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:00:58,145] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:00:58,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda40fb41-339e-4648-a2c8-cf059f3df029/dqc_reference/checkm_data
[2023-03-16 10:00:58,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:00:58,375] [INFO] Task started: CheckM
[2023-03-16 10:00:58,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30025/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30025/checkm_input OceanDNA-b30025/checkm_result
[2023-03-16 10:01:55,465] [INFO] Task succeeded: CheckM
[2023-03-16 10:01:55,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:01:55,481] [INFO] ===== Completeness check finished =====
[2023-03-16 10:01:55,481] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:01:55,481] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30025/markers.fasta)
[2023-03-16 10:01:55,482] [INFO] Task started: Blastn
[2023-03-16 10:01:55,482] [INFO] Running command: blastn -query OceanDNA-b30025/markers.fasta -db /var/lib/cwl/stgda40fb41-339e-4648-a2c8-cf059f3df029/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30025/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:01:56,484] [INFO] Task succeeded: Blastn
[2023-03-16 10:01:56,486] [INFO] Selected 20 target genomes.
[2023-03-16 10:01:56,486] [INFO] Target genome list was writen to OceanDNA-b30025/target_genomes_gtdb.txt
[2023-03-16 10:01:56,503] [INFO] Task started: fastANI
[2023-03-16 10:01:56,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg02dd5823-603e-4f05-9d82-a23cc7da5f58/OceanDNA-b30025.fa --refList OceanDNA-b30025/target_genomes_gtdb.txt --output OceanDNA-b30025/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:02:11,012] [INFO] Task succeeded: fastANI
[2023-03-16 10:02:11,023] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:02:11,023] [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_001458215.1	s__Shimia thalassica	97.6841	1111	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	96.93	96.93	0.94	0.94	2	conclusive
GCF_003990645.1	s__Shimia sediminis	78.1799	361	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114635.1	s__Shimia aestuarii	78.0336	300	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142085.1	s__Shimia gijangensis	77.8636	319	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223085.1	s__Shimia sp018223085	77.7357	262	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001292625.1	s__Shimia sp001292625	77.7238	261	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	77.6424	274	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014475.1	s__Shimia abyssi	77.438	230	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744095.1	s__Shimia sp017744095	77.4082	235	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	77.3239	270	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_004799325.1	s__Thalassobius vesicularis	77.1788	184	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708925.1	s__Thalassobius sp002708925	77.0158	161	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCF_013031405.1	s__Ruegeria sp013031405	76.9702	196	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009496005.1	s__Epibacterium litoralis	76.9685	139	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	76.9229	184	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	76.8308	162	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001518015.1	s__Epibacterium horizontis	76.7791	170	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172215.1	s__Ruegeria meonggei	76.7062	171	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458295.1	s__Ruegeria denitrificans	76.6559	186	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592335.1	s__Sulfitobacter_F sp017592335	76.1553	91	1150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:02:11,024] [INFO] GTDB search result was written to OceanDNA-b30025/result_gtdb.tsv
[2023-03-16 10:02:11,024] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:02:11,027] [INFO] DFAST_QC result json was written to OceanDNA-b30025/dqc_result.json
[2023-03-16 10:02:11,027] [INFO] DFAST_QC completed!
[2023-03-16 10:02:11,027] [INFO] Total running time: 0h1m55s