[2024-01-25 19:44:05,702] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:05,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:05,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c06dbbd-2a1a-4250-bb34-750beafe3875/dqc_reference
[2024-01-25 19:44:06,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:06,918] [INFO] Task started: Prodigal
[2024-01-25 19:44:06,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg205889a3-03b1-4145-bba1-12ba367b822d/GCF_010667575.1_ASM1066757v1_genomic.fna.gz | prodigal -d GCF_010667575.1_ASM1066757v1_genomic.fna/cds.fna -a GCF_010667575.1_ASM1066757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:20,392] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:20,392] [INFO] Task started: HMMsearch
[2024-01-25 19:44:20,392] [INFO] Running command: hmmsearch --tblout GCF_010667575.1_ASM1066757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c06dbbd-2a1a-4250-bb34-750beafe3875/dqc_reference/reference_markers.hmm GCF_010667575.1_ASM1066757v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:20,694] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:20,695] [INFO] Found 6/6 markers.
[2024-01-25 19:44:20,740] [INFO] Query marker FASTA was written to GCF_010667575.1_ASM1066757v1_genomic.fna/markers.fasta
[2024-01-25 19:44:20,740] [INFO] Task started: Blastn
[2024-01-25 19:44:20,740] [INFO] Running command: blastn -query GCF_010667575.1_ASM1066757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c06dbbd-2a1a-4250-bb34-750beafe3875/dqc_reference/reference_markers.fasta -out GCF_010667575.1_ASM1066757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:21,467] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:21,471] [INFO] Selected 21 target genomes.
[2024-01-25 19:44:21,472] [INFO] Target genome list was writen to GCF_010667575.1_ASM1066757v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:21,492] [INFO] Task started: fastANI
[2024-01-25 19:44:21,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg205889a3-03b1-4145-bba1-12ba367b822d/GCF_010667575.1_ASM1066757v1_genomic.fna.gz --refList GCF_010667575.1_ASM1066757v1_genomic.fna/target_genomes.txt --output GCF_010667575.1_ASM1066757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:37,283] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:37,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c06dbbd-2a1a-4250-bb34-750beafe3875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:37,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c06dbbd-2a1a-4250-bb34-750beafe3875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:37,296] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:37,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:37,296] [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
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	100.0	1572	1576	95	conclusive
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	78.6213	585	1576	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.5053	525	1576	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	78.443	565	1576	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	78.3969	570	1576	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	78.335	537	1576	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	78.3249	531	1576	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.1059	391	1576	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.0242	405	1576	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.969	365	1576	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.9353	400	1576	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	77.8509	369	1576	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.8281	475	1576	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.7958	386	1576	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.7658	386	1576	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.2406	306	1576	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.0136	173	1576	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.9985	174	1576	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9787	206	1576	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.8515	192	1576	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.4992	166	1576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:37,298] [INFO] DFAST Taxonomy check result was written to GCF_010667575.1_ASM1066757v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:37,298] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:37,299] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:37,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c06dbbd-2a1a-4250-bb34-750beafe3875/dqc_reference/checkm_data
[2024-01-25 19:44:37,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:37,345] [INFO] Task started: CheckM
[2024-01-25 19:44:37,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010667575.1_ASM1066757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010667575.1_ASM1066757v1_genomic.fna/checkm_input GCF_010667575.1_ASM1066757v1_genomic.fna/checkm_result
[2024-01-25 19:45:18,600] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:18,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:18,633] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:18,633] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:18,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010667575.1_ASM1066757v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:18,633] [INFO] Task started: Blastn
[2024-01-25 19:45:18,634] [INFO] Running command: blastn -query GCF_010667575.1_ASM1066757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c06dbbd-2a1a-4250-bb34-750beafe3875/dqc_reference/reference_markers_gtdb.fasta -out GCF_010667575.1_ASM1066757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:19,817] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:19,820] [INFO] Selected 20 target genomes.
[2024-01-25 19:45:19,820] [INFO] Target genome list was writen to GCF_010667575.1_ASM1066757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:19,840] [INFO] Task started: fastANI
[2024-01-25 19:45:19,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg205889a3-03b1-4145-bba1-12ba367b822d/GCF_010667575.1_ASM1066757v1_genomic.fna.gz --refList GCF_010667575.1_ASM1066757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010667575.1_ASM1066757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:36,787] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:36,801] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:36,801] [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_010667575.1	s__Sulfitobacter sediminilitoris	100.0	1572	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017854855.1	s__Sulfitobacter sp017854855	79.1038	656	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	78.8233	609	1576	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	78.7369	600	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622365.1	s__Sulfitobacter noctilucae	78.6087	583	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002405.1	s__Sulfitobacter sp013002405	78.5542	476	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	78.4842	539	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	78.4796	518	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_000622325.1	s__Sulfitobacter geojensis	78.4294	562	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_001886735.1	s__Sulfitobacter alexandrii	78.3279	516	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	78.3249	531	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003611275.1	s__Sulfitobacter sp001634775	78.1503	405	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_017743885.1	s__Sulfitobacter sp001635605	78.0078	439	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCA_017854675.1	s__Sulfitobacter sp017854675	78.0028	415	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.9753	364	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102535.1	s__Sulfitobacter delicatus	77.9461	400	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013346665.1	s__Sulfitobacter maritimus	77.8816	367	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014763045.1	s__Sulfitobacter aestuariivivens	77.8215	476	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	77.2406	306	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709405.1	s__Marinibacterium sp002709405	76.5771	245	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:36,803] [INFO] GTDB search result was written to GCF_010667575.1_ASM1066757v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:36,803] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:36,807] [INFO] DFAST_QC result json was written to GCF_010667575.1_ASM1066757v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:36,807] [INFO] DFAST_QC completed!
[2024-01-25 19:45:36,807] [INFO] Total running time: 0h1m31s