[2024-01-25 18:40:50,691] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:50,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:50,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f9ecb95-ddfb-4dc0-8a0e-5d2f2642d67b/dqc_reference
[2024-01-25 18:40:51,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:51,855] [INFO] Task started: Prodigal
[2024-01-25 18:40:51,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f42ba91-4f70-4a67-bf70-54db6ceb5b6c/GCF_000014045.1_ASM1404v1_genomic.fna.gz | prodigal -d GCF_000014045.1_ASM1404v1_genomic.fna/cds.fna -a GCF_000014045.1_ASM1404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:04,723] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:04,724] [INFO] Task started: HMMsearch
[2024-01-25 18:41:04,724] [INFO] Running command: hmmsearch --tblout GCF_000014045.1_ASM1404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f9ecb95-ddfb-4dc0-8a0e-5d2f2642d67b/dqc_reference/reference_markers.hmm GCF_000014045.1_ASM1404v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:05,020] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:05,021] [INFO] Found 6/6 markers.
[2024-01-25 18:41:05,074] [INFO] Query marker FASTA was written to GCF_000014045.1_ASM1404v1_genomic.fna/markers.fasta
[2024-01-25 18:41:05,074] [INFO] Task started: Blastn
[2024-01-25 18:41:05,075] [INFO] Running command: blastn -query GCF_000014045.1_ASM1404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f9ecb95-ddfb-4dc0-8a0e-5d2f2642d67b/dqc_reference/reference_markers.fasta -out GCF_000014045.1_ASM1404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:05,869] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:05,872] [INFO] Selected 18 target genomes.
[2024-01-25 18:41:05,872] [INFO] Target genome list was writen to GCF_000014045.1_ASM1404v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:05,878] [INFO] Task started: fastANI
[2024-01-25 18:41:05,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f42ba91-4f70-4a67-bf70-54db6ceb5b6c/GCF_000014045.1_ASM1404v1_genomic.fna.gz --refList GCF_000014045.1_ASM1404v1_genomic.fna/target_genomes.txt --output GCF_000014045.1_ASM1404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:20,922] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:20,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f9ecb95-ddfb-4dc0-8a0e-5d2f2642d67b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:20,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f9ecb95-ddfb-4dc0-8a0e-5d2f2642d67b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:20,934] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:41:20,935] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:20,935] [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 denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	100.0	1441	1441	95	conclusive
Roseobacter denitrificans	strain=DSM 7001	GCA_900113215.1	2434	2434	type	True	99.9777	1416	1441	95	conclusive
Roseobacter litoralis	strain=Och 149	GCA_000154785.2	42443	42443	type	True	88.5313	1181	1441	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	78.3155	477	1441	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.0787	409	1441	95	below_threshold
Roseobacter ponti	strain=DSM 106830	GCA_012932215.1	1891787	1891787	type	True	78.0479	434	1441	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.8087	347	1441	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.767	351	1441	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.7304	287	1441	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	77.4745	306	1441	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	77.4409	249	1441	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.44	293	1441	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.3998	283	1441	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.0491	267	1441	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9478	191	1441	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.9295	221	1441	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.7131	126	1441	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.4556	99	1441	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:20,938] [INFO] DFAST Taxonomy check result was written to GCF_000014045.1_ASM1404v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:20,938] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:20,939] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:20,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f9ecb95-ddfb-4dc0-8a0e-5d2f2642d67b/dqc_reference/checkm_data
[2024-01-25 18:41:20,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:20,988] [INFO] Task started: CheckM
[2024-01-25 18:41:20,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000014045.1_ASM1404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000014045.1_ASM1404v1_genomic.fna/checkm_input GCF_000014045.1_ASM1404v1_genomic.fna/checkm_result
[2024-01-25 18:42:09,286] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:09,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:09,300] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:09,300] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:09,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000014045.1_ASM1404v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:09,301] [INFO] Task started: Blastn
[2024-01-25 18:42:09,301] [INFO] Running command: blastn -query GCF_000014045.1_ASM1404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f9ecb95-ddfb-4dc0-8a0e-5d2f2642d67b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000014045.1_ASM1404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:10,755] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:10,757] [INFO] Selected 17 target genomes.
[2024-01-25 18:42:10,757] [INFO] Target genome list was writen to GCF_000014045.1_ASM1404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:10,766] [INFO] Task started: fastANI
[2024-01-25 18:42:10,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f42ba91-4f70-4a67-bf70-54db6ceb5b6c/GCF_000014045.1_ASM1404v1_genomic.fna.gz --refList GCF_000014045.1_ASM1404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000014045.1_ASM1404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:25,742] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:25,753] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:25,754] [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_000014045.1	s__Roseobacter denitrificans	100.0	1441	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_000154785.2	s__Roseobacter litoralis	88.5313	1181	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644665.1	s__Roseobacter sp015644665	78.5687	532	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014337925.1	s__Roseobacter litoralis_A	78.4405	503	1441	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	78.3073	478	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	78.1048	406	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	78.0513	336	1441	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	77.8465	377	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.7999	348	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003611275.1	s__Sulfitobacter sp001634775	77.756	333	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	77.5335	362	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	77.4676	306	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112755.1	s__Sulfitobacter brevis	77.4409	249	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113435.1	s__Sulfitobacter dubius	77.44	293	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.4105	282	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210095.1	s__Marinibacterium profundimaris	77.1385	286	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110425.1	s__Salinihabitans flavidus	76.936	211	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salinihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:25,755] [INFO] GTDB search result was written to GCF_000014045.1_ASM1404v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:25,756] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:25,760] [INFO] DFAST_QC result json was written to GCF_000014045.1_ASM1404v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:25,760] [INFO] DFAST_QC completed!
[2024-01-25 18:42:25,760] [INFO] Total running time: 0h1m35s