[2024-01-24 13:35:26,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:26,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:26,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgebc09691-5ccd-4ca8-8f03-ffac7fc7f45f/dqc_reference
[2024-01-24 13:35:27,998] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:28,000] [INFO] Task started: Prodigal
[2024-01-24 13:35:28,000] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e52289d-43d7-4bc0-a868-a6943b661e37/GCF_021228235.1_ASM2122823v1_genomic.fna.gz | prodigal -d GCF_021228235.1_ASM2122823v1_genomic.fna/cds.fna -a GCF_021228235.1_ASM2122823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:41,572] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:41,573] [INFO] Task started: HMMsearch
[2024-01-24 13:35:41,573] [INFO] Running command: hmmsearch --tblout GCF_021228235.1_ASM2122823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebc09691-5ccd-4ca8-8f03-ffac7fc7f45f/dqc_reference/reference_markers.hmm GCF_021228235.1_ASM2122823v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:41,843] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:41,845] [INFO] Found 6/6 markers.
[2024-01-24 13:35:41,885] [INFO] Query marker FASTA was written to GCF_021228235.1_ASM2122823v1_genomic.fna/markers.fasta
[2024-01-24 13:35:41,886] [INFO] Task started: Blastn
[2024-01-24 13:35:41,886] [INFO] Running command: blastn -query GCF_021228235.1_ASM2122823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebc09691-5ccd-4ca8-8f03-ffac7fc7f45f/dqc_reference/reference_markers.fasta -out GCF_021228235.1_ASM2122823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:42,599] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:42,604] [INFO] Selected 16 target genomes.
[2024-01-24 13:35:42,604] [INFO] Target genome list was writen to GCF_021228235.1_ASM2122823v1_genomic.fna/target_genomes.txt
[2024-01-24 13:35:42,622] [INFO] Task started: fastANI
[2024-01-24 13:35:42,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e52289d-43d7-4bc0-a868-a6943b661e37/GCF_021228235.1_ASM2122823v1_genomic.fna.gz --refList GCF_021228235.1_ASM2122823v1_genomic.fna/target_genomes.txt --output GCF_021228235.1_ASM2122823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:35:57,188] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:57,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebc09691-5ccd-4ca8-8f03-ffac7fc7f45f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:35:57,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebc09691-5ccd-4ca8-8f03-ffac7fc7f45f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:35:57,208] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:35:57,208] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:35:57,209] [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
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	100.0	1417	1418	95	conclusive
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	83.4282	997	1418	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	81.7325	890	1418	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.7961	623	1418	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.776	641	1418	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	78.7182	622	1418	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.6423	626	1418	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	78.6059	558	1418	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	78.5327	536	1418	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	78.3683	509	1418	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.8538	377	1418	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.7724	405	1418	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.578	395	1418	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	77.507	297	1418	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.0747	316	1418	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.8166	186	1418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:35:57,210] [INFO] DFAST Taxonomy check result was written to GCF_021228235.1_ASM2122823v1_genomic.fna/tc_result.tsv
[2024-01-24 13:35:57,211] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:35:57,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:35:57,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebc09691-5ccd-4ca8-8f03-ffac7fc7f45f/dqc_reference/checkm_data
[2024-01-24 13:35:57,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:35:57,256] [INFO] Task started: CheckM
[2024-01-24 13:35:57,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021228235.1_ASM2122823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021228235.1_ASM2122823v1_genomic.fna/checkm_input GCF_021228235.1_ASM2122823v1_genomic.fna/checkm_result
[2024-01-24 13:36:39,169] [INFO] Task succeeded: CheckM
[2024-01-24 13:36:39,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:36:39,191] [INFO] ===== Completeness check finished =====
[2024-01-24 13:36:39,192] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:36:39,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021228235.1_ASM2122823v1_genomic.fna/markers.fasta)
[2024-01-24 13:36:39,192] [INFO] Task started: Blastn
[2024-01-24 13:36:39,193] [INFO] Running command: blastn -query GCF_021228235.1_ASM2122823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebc09691-5ccd-4ca8-8f03-ffac7fc7f45f/dqc_reference/reference_markers_gtdb.fasta -out GCF_021228235.1_ASM2122823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:40,251] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:40,255] [INFO] Selected 9 target genomes.
[2024-01-24 13:36:40,255] [INFO] Target genome list was writen to GCF_021228235.1_ASM2122823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:36:40,266] [INFO] Task started: fastANI
[2024-01-24 13:36:40,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e52289d-43d7-4bc0-a868-a6943b661e37/GCF_021228235.1_ASM2122823v1_genomic.fna.gz --refList GCF_021228235.1_ASM2122823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021228235.1_ASM2122823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:50,121] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:50,133] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:36:50,133] [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_000473205.1	s__Pseudophaeobacter arcticus	83.444	995	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479575.1	s__Pseudophaeobacter sp905479575	82.4158	902	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900313025.1	s__Pseudophaeobacter sp900313025	81.823	941	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002087335.1	s__Pseudophaeobacter leonis	81.7243	891	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294455.1	s__Pseudophaeobacter sp001294455	81.5493	898	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	98.13	98.13	0.97	0.97	2	-
GCF_001457775.1	s__Pseudophaeobacter sp001457775	81.2387	820	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665415.1	s__Pseudophaeobacter sp015665415	81.2201	883	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152965.1	s__Pseudophaeobacter sp000152965	80.9411	854	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	98.26	98.26	0.93	0.93	2	-
GCA_013214575.1	s__Parasedimentitalea sp013214575	78.7064	561	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:50,135] [INFO] GTDB search result was written to GCF_021228235.1_ASM2122823v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:50,136] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:50,139] [INFO] DFAST_QC result json was written to GCF_021228235.1_ASM2122823v1_genomic.fna/dqc_result.json
[2024-01-24 13:36:50,140] [INFO] DFAST_QC completed!
[2024-01-24 13:36:50,140] [INFO] Total running time: 0h1m23s