[2024-01-24 13:21:55,569] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:55,571] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:55,572] [INFO] DQC Reference Directory: /var/lib/cwl/stg756121e8-d87c-48d5-8ecf-90fc6049893d/dqc_reference
[2024-01-24 13:21:56,848] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:56,849] [INFO] Task started: Prodigal
[2024-01-24 13:21:56,850] [INFO] Running command: gunzip -c /var/lib/cwl/stg56aad41e-405a-44d3-92ce-bc8ef7724ea0/GCF_012932215.1_ASM1293221v1_genomic.fna.gz | prodigal -d GCF_012932215.1_ASM1293221v1_genomic.fna/cds.fna -a GCF_012932215.1_ASM1293221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:08,922] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:08,923] [INFO] Task started: HMMsearch
[2024-01-24 13:22:08,923] [INFO] Running command: hmmsearch --tblout GCF_012932215.1_ASM1293221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg756121e8-d87c-48d5-8ecf-90fc6049893d/dqc_reference/reference_markers.hmm GCF_012932215.1_ASM1293221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:09,203] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:09,204] [INFO] Found 6/6 markers.
[2024-01-24 13:22:09,246] [INFO] Query marker FASTA was written to GCF_012932215.1_ASM1293221v1_genomic.fna/markers.fasta
[2024-01-24 13:22:09,246] [INFO] Task started: Blastn
[2024-01-24 13:22:09,246] [INFO] Running command: blastn -query GCF_012932215.1_ASM1293221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg756121e8-d87c-48d5-8ecf-90fc6049893d/dqc_reference/reference_markers.fasta -out GCF_012932215.1_ASM1293221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:10,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:10,280] [INFO] Selected 24 target genomes.
[2024-01-24 13:22:10,281] [INFO] Target genome list was writen to GCF_012932215.1_ASM1293221v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:10,289] [INFO] Task started: fastANI
[2024-01-24 13:22:10,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg56aad41e-405a-44d3-92ce-bc8ef7724ea0/GCF_012932215.1_ASM1293221v1_genomic.fna.gz --refList GCF_012932215.1_ASM1293221v1_genomic.fna/target_genomes.txt --output GCF_012932215.1_ASM1293221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:28,200] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:28,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg756121e8-d87c-48d5-8ecf-90fc6049893d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:28,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg756121e8-d87c-48d5-8ecf-90fc6049893d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:28,219] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:28,219] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:28,220] [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
Roseobacter ponti	strain=DSM 106830	GCA_012932215.1	1891787	1891787	type	True	100.0	1320	1320	95	conclusive
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	78.4199	476	1320	95	below_threshold
Roseobacter denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	78.1624	415	1320	95	below_threshold
Roseobacter denitrificans	strain=DSM 7001	GCA_900113215.1	2434	2434	type	True	78.1362	409	1320	95	below_threshold
Roseobacter litoralis	strain=Och 149	GCA_000154785.2	42443	42443	type	True	77.8971	356	1320	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.4729	306	1320	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.4088	278	1320	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	77.3912	251	1320	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.3803	334	1320	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.3713	307	1320	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.3166	320	1320	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.2936	347	1320	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.2478	233	1320	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.1724	283	1320	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.1553	313	1320	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.0334	209	1320	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.018	256	1320	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	76.8293	187	1320	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.8242	276	1320	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.7441	208	1320	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.7423	277	1320	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.6633	162	1320	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.6631	161	1320	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.4198	204	1320	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:28,221] [INFO] DFAST Taxonomy check result was written to GCF_012932215.1_ASM1293221v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:28,222] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:28,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:28,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg756121e8-d87c-48d5-8ecf-90fc6049893d/dqc_reference/checkm_data
[2024-01-24 13:22:28,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:28,263] [INFO] Task started: CheckM
[2024-01-24 13:22:28,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012932215.1_ASM1293221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012932215.1_ASM1293221v1_genomic.fna/checkm_input GCF_012932215.1_ASM1293221v1_genomic.fna/checkm_result
[2024-01-24 13:23:08,190] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:08,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:08,208] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:08,208] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:08,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012932215.1_ASM1293221v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:08,209] [INFO] Task started: Blastn
[2024-01-24 13:23:08,209] [INFO] Running command: blastn -query GCF_012932215.1_ASM1293221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg756121e8-d87c-48d5-8ecf-90fc6049893d/dqc_reference/reference_markers_gtdb.fasta -out GCF_012932215.1_ASM1293221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:09,852] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:09,855] [INFO] Selected 20 target genomes.
[2024-01-24 13:23:09,855] [INFO] Target genome list was writen to GCF_012932215.1_ASM1293221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:09,868] [INFO] Task started: fastANI
[2024-01-24 13:23:09,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg56aad41e-405a-44d3-92ce-bc8ef7724ea0/GCF_012932215.1_ASM1293221v1_genomic.fna.gz --refList GCF_012932215.1_ASM1293221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012932215.1_ASM1293221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:25,277] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:25,293] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:25,294] [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_012932215.1	s__Roseobacter ponti	100.0	1320	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015644665.1	s__Roseobacter sp015644665	78.5722	561	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811755.1	s__Roseobacter cerasinus	78.4199	476	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014045.1	s__Roseobacter denitrificans	78.1535	416	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014337925.1	s__Roseobacter litoralis_A	78.0289	431	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	77.9245	420	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	77.8172	378	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	77.7104	335	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCA_013139555.1	s__Sulfitobacter sp013139555	77.4293	192	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	77.3969	332	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_000203975.2	s__Leisingera sp000203975	77.3562	301	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_900102535.1	s__Sulfitobacter delicatus	77.3175	320	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.3017	344	1320	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_900109035.1	s__Cribrihabitans marinus	77.2972	347	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005938215.1	s__Ruegeria sediminis	77.1911	281	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	77.1703	311	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_002210095.1	s__Marinibacterium profundimaris	77.1072	329	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	77.0357	289	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003646465.1	s__Chachezhania antarctica	76.8812	235	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803475.1	s__Aliishimia ponticola	76.7663	276	1320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:25,296] [INFO] GTDB search result was written to GCF_012932215.1_ASM1293221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:25,297] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:25,301] [INFO] DFAST_QC result json was written to GCF_012932215.1_ASM1293221v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:25,302] [INFO] DFAST_QC completed!
[2024-01-24 13:23:25,302] [INFO] Total running time: 0h1m30s