[2023-06-13 14:06:10,178] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:06:10,181] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:06:10,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg52e7b1d4-b755-46e3-86ff-d9eb8732ff00/dqc_reference
[2023-06-13 14:06:11,548] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:06:11,549] [INFO] Task started: Prodigal
[2023-06-13 14:06:11,549] [INFO] Running command: gunzip -c /var/lib/cwl/stge76d919a-e371-405d-87eb-7116a5f65b82/GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna.gz | prodigal -d GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/cds.fna -a GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:06:24,366] [INFO] Task succeeded: Prodigal
[2023-06-13 14:06:24,367] [INFO] Task started: HMMsearch
[2023-06-13 14:06:24,367] [INFO] Running command: hmmsearch --tblout GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52e7b1d4-b755-46e3-86ff-d9eb8732ff00/dqc_reference/reference_markers.hmm GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:06:24,672] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:06:24,674] [INFO] Found 6/6 markers.
[2023-06-13 14:06:24,711] [INFO] Query marker FASTA was written to GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/markers.fasta
[2023-06-13 14:06:24,711] [INFO] Task started: Blastn
[2023-06-13 14:06:24,711] [INFO] Running command: blastn -query GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52e7b1d4-b755-46e3-86ff-d9eb8732ff00/dqc_reference/reference_markers.fasta -out GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:06:25,468] [INFO] Task succeeded: Blastn
[2023-06-13 14:06:25,472] [INFO] Selected 30 target genomes.
[2023-06-13 14:06:25,472] [INFO] Target genome list was writen to GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/target_genomes.txt
[2023-06-13 14:06:25,482] [INFO] Task started: fastANI
[2023-06-13 14:06:25,482] [INFO] Running command: fastANI --query /var/lib/cwl/stge76d919a-e371-405d-87eb-7116a5f65b82/GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna.gz --refList GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/target_genomes.txt --output GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:06:45,814] [INFO] Task succeeded: fastANI
[2023-06-13 14:06:45,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52e7b1d4-b755-46e3-86ff-d9eb8732ff00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:06:45,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52e7b1d4-b755-46e3-86ff-d9eb8732ff00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:06:45,838] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:06:45,839] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:06:45,839] [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	76.854	146	1282	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	76.7002	104	1282	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.6262	145	1282	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.6251	156	1282	95	below_threshold
Litoreibacter arenae	strain=DSM 19593	GCA_000442275.2	491388	491388	type	True	76.6213	107	1282	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	76.6105	140	1282	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.556	64	1282	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	76.4957	98	1282	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	76.4592	124	1282	95	below_threshold
Aliiroseovarius crassostreae	strain=DSM 16950	GCA_900116725.1	154981	154981	type	True	76.4442	100	1282	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	76.4137	128	1282	95	below_threshold
Aliiroseovarius crassostreae	strain=CV919-312	GCA_001307765.1	154981	154981	type	True	76.3757	99	1282	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.3477	84	1282	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	76.2936	118	1282	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	76.2836	99	1282	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.2757	111	1282	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	76.2124	93	1282	95	below_threshold
Oceaniglobus ichthyenteri	strain=YLY08	GCA_003057885.1	2136177	2136177	type	True	76.2006	108	1282	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	76.1962	86	1282	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	76.1773	91	1282	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.1771	96	1282	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	76.1696	92	1282	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.1489	93	1282	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	76.1012	85	1282	95	below_threshold
Paracoccus jeotgali	strain=CBA4604	GCA_002865605.1	2065379	2065379	type	True	76.0201	66	1282	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.0197	93	1282	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.0144	80	1282	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.9471	78	1282	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	75.8875	88	1282	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	75.854	71	1282	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:06:45,842] [INFO] DFAST Taxonomy check result was written to GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/tc_result.tsv
[2023-06-13 14:06:45,842] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:06:45,842] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:06:45,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52e7b1d4-b755-46e3-86ff-d9eb8732ff00/dqc_reference/checkm_data
[2023-06-13 14:06:45,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:06:45,886] [INFO] Task started: CheckM
[2023-06-13 14:06:45,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/checkm_input GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/checkm_result
[2023-06-13 14:07:26,324] [INFO] Task succeeded: CheckM
[2023-06-13 14:07:26,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 14:07:26,350] [INFO] ===== Completeness check finished =====
[2023-06-13 14:07:26,350] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:07:26,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/markers.fasta)
[2023-06-13 14:07:26,351] [INFO] Task started: Blastn
[2023-06-13 14:07:26,351] [INFO] Running command: blastn -query GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52e7b1d4-b755-46e3-86ff-d9eb8732ff00/dqc_reference/reference_markers_gtdb.fasta -out GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:07:27,637] [INFO] Task succeeded: Blastn
[2023-06-13 14:07:27,642] [INFO] Selected 26 target genomes.
[2023-06-13 14:07:27,642] [INFO] Target genome list was writen to GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:07:27,654] [INFO] Task started: fastANI
[2023-06-13 14:07:27,654] [INFO] Running command: fastANI --query /var/lib/cwl/stge76d919a-e371-405d-87eb-7116a5f65b82/GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna.gz --refList GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:07:42,890] [INFO] Task succeeded: fastANI
[2023-06-13 14:07:42,915] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 14:07:42,916] [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_014075275.1	s__Boseongicola sp014075275	77.3157	136	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.87	99.87	0.99	0.99	2	-
GCA_013002465.1	s__JABDJO01 sp013002465	77.0944	289	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184815.1	s__Boseongicola aestuarii	76.8385	147	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	76.6414	144	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	76.6341	114	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000442275.2	s__Litoreibacter arenae	76.6213	107	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009830125.1	s__GH1-50 sp009830125	76.612	157	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	76.5327	109	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003245.1	s__JABDJX01 sp013003245	76.5115	185	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592335.1	s__Sulfitobacter_F sp017592335	76.4489	125	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148765.1	s__Silicimonas algicola	76.4468	126	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905479635.1	s__Boseongicola sp905479635	76.3496	93	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004360145.1	s__Aliiroseovarius marinus	76.2836	99	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	76.2757	111	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	76.2546	119	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	76.2542	141	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	76.1802	77	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003172915.1	s__Fluviibacterium sp003172915	76.1445	74	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018263905.1	s__Loktanella sp018263905	76.1322	103	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443995.1	s__ETT8 sp003443995	76.1321	94	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214635.1	s__JABSSC01 sp013214635	76.0928	111	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABSSC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	76.0859	108	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	76.0834	86	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCA_013042895.1	s__Boseongicola sp013042895	75.9267	57	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	98.28	98.28	0.61	0.61	2	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	75.763	88	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCA_009843725.1	s__JABDJO01 sp009843725	75.6959	75	1282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:07:42,918] [INFO] GTDB search result was written to GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:07:42,918] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:07:42,924] [INFO] DFAST_QC result json was written to GCA_938005545.1_H2_Bin_Bin_74_1_genomic.fna/dqc_result.json
[2023-06-13 14:07:42,924] [INFO] DFAST_QC completed!
[2023-06-13 14:07:42,924] [INFO] Total running time: 0h1m33s