[2024-01-25 18:33:21,112] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:33:21,113] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:33:21,113] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe8a3624-c478-46c3-a72d-927d5678c7df/dqc_reference
[2024-01-25 18:33:22,252] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:33:22,253] [INFO] Task started: Prodigal
[2024-01-25 18:33:22,253] [INFO] Running command: gunzip -c /var/lib/cwl/stg013c781e-44de-4de1-99a5-c26b8918254e/GCF_027925385.1_ASM2792538v1_genomic.fna.gz | prodigal -d GCF_027925385.1_ASM2792538v1_genomic.fna/cds.fna -a GCF_027925385.1_ASM2792538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:33:34,236] [INFO] Task succeeded: Prodigal
[2024-01-25 18:33:34,237] [INFO] Task started: HMMsearch
[2024-01-25 18:33:34,237] [INFO] Running command: hmmsearch --tblout GCF_027925385.1_ASM2792538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe8a3624-c478-46c3-a72d-927d5678c7df/dqc_reference/reference_markers.hmm GCF_027925385.1_ASM2792538v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:33:34,501] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:33:34,502] [INFO] Found 6/6 markers.
[2024-01-25 18:33:34,539] [INFO] Query marker FASTA was written to GCF_027925385.1_ASM2792538v1_genomic.fna/markers.fasta
[2024-01-25 18:33:34,539] [INFO] Task started: Blastn
[2024-01-25 18:33:34,539] [INFO] Running command: blastn -query GCF_027925385.1_ASM2792538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe8a3624-c478-46c3-a72d-927d5678c7df/dqc_reference/reference_markers.fasta -out GCF_027925385.1_ASM2792538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:33:35,379] [INFO] Task succeeded: Blastn
[2024-01-25 18:33:35,382] [INFO] Selected 14 target genomes.
[2024-01-25 18:33:35,382] [INFO] Target genome list was writen to GCF_027925385.1_ASM2792538v1_genomic.fna/target_genomes.txt
[2024-01-25 18:33:35,411] [INFO] Task started: fastANI
[2024-01-25 18:33:35,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg013c781e-44de-4de1-99a5-c26b8918254e/GCF_027925385.1_ASM2792538v1_genomic.fna.gz --refList GCF_027925385.1_ASM2792538v1_genomic.fna/target_genomes.txt --output GCF_027925385.1_ASM2792538v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:33:48,325] [INFO] Task succeeded: fastANI
[2024-01-25 18:33:48,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe8a3624-c478-46c3-a72d-927d5678c7df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:33:48,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe8a3624-c478-46c3-a72d-927d5678c7df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:33:48,334] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:33:48,334] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:33:48,335] [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
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	82.5546	839	1490	95	below_threshold
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	79.7757	591	1490	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	79.6793	599	1490	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	79.639	577	1490	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	79.6288	594	1490	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	79.5976	607	1490	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	79.595	574	1490	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	79.5173	557	1490	95	below_threshold
Methylocystis heyeri	strain=H2	GCA_004802635.2	391905	391905	type	True	78.9753	512	1490	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	77.0901	210	1490	95	below_threshold
Saliniramus fredricksonii	strain=HL-109	GCA_900094735.1	1653334	1653334	type	True	77.0753	197	1490	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	76.9317	233	1490	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.8362	250	1490	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.6411	185	1490	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:33:48,336] [INFO] DFAST Taxonomy check result was written to GCF_027925385.1_ASM2792538v1_genomic.fna/tc_result.tsv
[2024-01-25 18:33:48,336] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:33:48,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:33:48,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe8a3624-c478-46c3-a72d-927d5678c7df/dqc_reference/checkm_data
[2024-01-25 18:33:48,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:33:48,382] [INFO] Task started: CheckM
[2024-01-25 18:33:48,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027925385.1_ASM2792538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027925385.1_ASM2792538v1_genomic.fna/checkm_input GCF_027925385.1_ASM2792538v1_genomic.fna/checkm_result
[2024-01-25 18:34:24,944] [INFO] Task succeeded: CheckM
[2024-01-25 18:34:24,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:34:24,964] [INFO] ===== Completeness check finished =====
[2024-01-25 18:34:24,964] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:34:24,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027925385.1_ASM2792538v1_genomic.fna/markers.fasta)
[2024-01-25 18:34:24,965] [INFO] Task started: Blastn
[2024-01-25 18:34:24,965] [INFO] Running command: blastn -query GCF_027925385.1_ASM2792538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe8a3624-c478-46c3-a72d-927d5678c7df/dqc_reference/reference_markers_gtdb.fasta -out GCF_027925385.1_ASM2792538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:34:26,481] [INFO] Task succeeded: Blastn
[2024-01-25 18:34:26,483] [INFO] Selected 7 target genomes.
[2024-01-25 18:34:26,483] [INFO] Target genome list was writen to GCF_027925385.1_ASM2792538v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:34:26,496] [INFO] Task started: fastANI
[2024-01-25 18:34:26,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg013c781e-44de-4de1-99a5-c26b8918254e/GCF_027925385.1_ASM2792538v1_genomic.fna.gz --refList GCF_027925385.1_ASM2792538v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027925385.1_ASM2792538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:34:35,411] [INFO] Task succeeded: fastANI
[2024-01-25 18:34:35,417] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:34:35,417] [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_016745395.1	s__Methylocystis sp016745395	96.7678	1253	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011058845.1	s__Methylocystis sp011058845	90.4312	1117	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000283235.1	s__Methylocystis parvus	82.4771	848	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003963405.1	s__Methylocystis sp003963405	82.2056	756	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002929055.1	s__Methylocystis sp002929055	81.8836	702	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188155.2	s__Methylocystis sp000188155	81.6755	758	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015709525.1	s__Methylocystis sp015709525	79.7727	567	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:34:35,419] [INFO] GTDB search result was written to GCF_027925385.1_ASM2792538v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:34:35,420] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:34:35,423] [INFO] DFAST_QC result json was written to GCF_027925385.1_ASM2792538v1_genomic.fna/dqc_result.json
[2024-01-25 18:34:35,424] [INFO] DFAST_QC completed!
[2024-01-25 18:34:35,424] [INFO] Total running time: 0h1m14s