[2024-01-25 18:06:05,788] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:05,790] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:05,790] [INFO] DQC Reference Directory: /var/lib/cwl/stgac48f0b1-9311-40bf-bc31-3af7d08ce3a5/dqc_reference
[2024-01-25 18:06:06,904] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:06,904] [INFO] Task started: Prodigal
[2024-01-25 18:06:06,905] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c946882-b3f9-491f-9626-94dd0470d1bb/GCF_013350005.1_ASM1335000v1_genomic.fna.gz | prodigal -d GCF_013350005.1_ASM1335000v1_genomic.fna/cds.fna -a GCF_013350005.1_ASM1335000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:16,286] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:16,286] [INFO] Task started: HMMsearch
[2024-01-25 18:06:16,286] [INFO] Running command: hmmsearch --tblout GCF_013350005.1_ASM1335000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac48f0b1-9311-40bf-bc31-3af7d08ce3a5/dqc_reference/reference_markers.hmm GCF_013350005.1_ASM1335000v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:16,500] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:16,501] [INFO] Found 6/6 markers.
[2024-01-25 18:06:16,532] [INFO] Query marker FASTA was written to GCF_013350005.1_ASM1335000v1_genomic.fna/markers.fasta
[2024-01-25 18:06:16,532] [INFO] Task started: Blastn
[2024-01-25 18:06:16,532] [INFO] Running command: blastn -query GCF_013350005.1_ASM1335000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac48f0b1-9311-40bf-bc31-3af7d08ce3a5/dqc_reference/reference_markers.fasta -out GCF_013350005.1_ASM1335000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:17,261] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:17,264] [INFO] Selected 12 target genomes.
[2024-01-25 18:06:17,265] [INFO] Target genome list was writen to GCF_013350005.1_ASM1335000v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:17,271] [INFO] Task started: fastANI
[2024-01-25 18:06:17,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c946882-b3f9-491f-9626-94dd0470d1bb/GCF_013350005.1_ASM1335000v1_genomic.fna.gz --refList GCF_013350005.1_ASM1335000v1_genomic.fna/target_genomes.txt --output GCF_013350005.1_ASM1335000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:28,845] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:28,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac48f0b1-9311-40bf-bc31-3af7d08ce3a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:28,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac48f0b1-9311-40bf-bc31-3af7d08ce3a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:28,854] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:28,854] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:28,854] [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 silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	100.0	1249	1252	95	conclusive
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	94.1743	1051	1252	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	92.8609	990	1252	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	79.793	598	1252	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	78.8967	520	1252	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	78.8877	520	1252	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	77.5198	261	1252	95	below_threshold
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_002937075.1	333368	333368	type	True	77.3001	266	1252	95	below_threshold
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_014197735.1	333368	333368	type	True	77.2805	266	1252	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	76.7786	172	1252	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	76.7718	221	1252	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	76.561	234	1252	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:28,855] [INFO] DFAST Taxonomy check result was written to GCF_013350005.1_ASM1335000v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:28,856] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:28,856] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:28,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac48f0b1-9311-40bf-bc31-3af7d08ce3a5/dqc_reference/checkm_data
[2024-01-25 18:06:28,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:28,896] [INFO] Task started: CheckM
[2024-01-25 18:06:28,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013350005.1_ASM1335000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013350005.1_ASM1335000v1_genomic.fna/checkm_input GCF_013350005.1_ASM1335000v1_genomic.fna/checkm_result
[2024-01-25 18:06:58,344] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:58,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:06:58,362] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:58,362] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:58,362] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013350005.1_ASM1335000v1_genomic.fna/markers.fasta)
[2024-01-25 18:06:58,362] [INFO] Task started: Blastn
[2024-01-25 18:06:58,362] [INFO] Running command: blastn -query GCF_013350005.1_ASM1335000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac48f0b1-9311-40bf-bc31-3af7d08ce3a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_013350005.1_ASM1335000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:59,637] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:59,640] [INFO] Selected 8 target genomes.
[2024-01-25 18:06:59,640] [INFO] Target genome list was writen to GCF_013350005.1_ASM1335000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:59,648] [INFO] Task started: fastANI
[2024-01-25 18:06:59,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c946882-b3f9-491f-9626-94dd0470d1bb/GCF_013350005.1_ASM1335000v1_genomic.fna.gz --refList GCF_013350005.1_ASM1335000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013350005.1_ASM1335000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:07,679] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:07,686] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:07,686] [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_013350005.1	s__Methylocystis sp013350005	100.0	1249	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	96.16	96.16	0.88	0.88	2	conclusive
GCF_003722355.1	s__Methylocystis hirsuta	94.1843	1050	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	95.95	95.95	0.95	0.95	2	-
GCF_000304315.1	s__Methylocystis sp000304315	92.9031	999	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372845.1	s__Methylocystis rosea	92.8646	989	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	95.62	95.24	0.85	0.83	5	-
GCA_009773555.1	s__Methylocystis sp009773555	92.7934	976	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	99.69	99.47	0.95	0.93	3	-
GCF_015709525.1	s__Methylocystis sp015709525	92.7005	1023	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015709515.1	s__Methylocystis sp015709515	92.5776	1028	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869435.1	s__Methylocystis sp016869435	85.1587	760	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:07,687] [INFO] GTDB search result was written to GCF_013350005.1_ASM1335000v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:07,688] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:07,691] [INFO] DFAST_QC result json was written to GCF_013350005.1_ASM1335000v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:07,692] [INFO] DFAST_QC completed!
[2024-01-25 18:07:07,692] [INFO] Total running time: 0h1m2s