[2024-01-24 13:40:45,681] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:45,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:45,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c2aa3b0-959a-4208-ba64-879a4d518425/dqc_reference
[2024-01-24 13:40:46,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:46,990] [INFO] Task started: Prodigal
[2024-01-24 13:40:46,990] [INFO] Running command: gunzip -c /var/lib/cwl/stge8a177eb-e64d-484e-b419-9cd80e42fa5f/GCF_004802635.2_ASM480263v2_genomic.fna.gz | prodigal -d GCF_004802635.2_ASM480263v2_genomic.fna/cds.fna -a GCF_004802635.2_ASM480263v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:01,327] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:01,328] [INFO] Task started: HMMsearch
[2024-01-24 13:41:01,328] [INFO] Running command: hmmsearch --tblout GCF_004802635.2_ASM480263v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c2aa3b0-959a-4208-ba64-879a4d518425/dqc_reference/reference_markers.hmm GCF_004802635.2_ASM480263v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:01,627] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:01,628] [INFO] Found 6/6 markers.
[2024-01-24 13:41:01,669] [INFO] Query marker FASTA was written to GCF_004802635.2_ASM480263v2_genomic.fna/markers.fasta
[2024-01-24 13:41:01,669] [INFO] Task started: Blastn
[2024-01-24 13:41:01,669] [INFO] Running command: blastn -query GCF_004802635.2_ASM480263v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c2aa3b0-959a-4208-ba64-879a4d518425/dqc_reference/reference_markers.fasta -out GCF_004802635.2_ASM480263v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:02,649] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:02,653] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:02,654] [INFO] Target genome list was writen to GCF_004802635.2_ASM480263v2_genomic.fna/target_genomes.txt
[2024-01-24 13:41:02,682] [INFO] Task started: fastANI
[2024-01-24 13:41:02,682] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a177eb-e64d-484e-b419-9cd80e42fa5f/GCF_004802635.2_ASM480263v2_genomic.fna.gz --refList GCF_004802635.2_ASM480263v2_genomic.fna/target_genomes.txt --output GCF_004802635.2_ASM480263v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:17,348] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:17,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c2aa3b0-959a-4208-ba64-879a4d518425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:17,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c2aa3b0-959a-4208-ba64-879a4d518425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:17,368] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:17,368] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:17,368] [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 heyeri	strain=H2	GCA_004802635.2	391905	391905	type	True	100.0	1573	1575	95	conclusive
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	78.9089	544	1575	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	78.9023	552	1575	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	78.8118	503	1575	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	78.7943	485	1575	95	below_threshold
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	78.555	421	1575	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	78.5138	500	1575	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	78.3296	401	1575	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	78.2585	386	1575	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	77.6195	307	1575	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	77.3454	171	1575	95	below_threshold
Saliniramus fredricksonii	strain=HL-109	GCA_900094735.1	1653334	1653334	type	True	77.138	151	1575	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	77.1017	249	1575	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	76.9014	311	1575	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	76.8523	194	1575	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.533	239	1575	95	below_threshold
Devosia equisanguinis	strain=CIP 111628	GCA_900631955.1	2490941	2490941	type	True	76.1778	99	1575	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:17,370] [INFO] DFAST Taxonomy check result was written to GCF_004802635.2_ASM480263v2_genomic.fna/tc_result.tsv
[2024-01-24 13:41:17,370] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:17,370] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:17,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c2aa3b0-959a-4208-ba64-879a4d518425/dqc_reference/checkm_data
[2024-01-24 13:41:17,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:17,417] [INFO] Task started: CheckM
[2024-01-24 13:41:17,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004802635.2_ASM480263v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004802635.2_ASM480263v2_genomic.fna/checkm_input GCF_004802635.2_ASM480263v2_genomic.fna/checkm_result
[2024-01-24 13:41:59,636] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:59,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:59,660] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:59,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:59,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004802635.2_ASM480263v2_genomic.fna/markers.fasta)
[2024-01-24 13:41:59,661] [INFO] Task started: Blastn
[2024-01-24 13:41:59,661] [INFO] Running command: blastn -query GCF_004802635.2_ASM480263v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c2aa3b0-959a-4208-ba64-879a4d518425/dqc_reference/reference_markers_gtdb.fasta -out GCF_004802635.2_ASM480263v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:01,615] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:01,620] [INFO] Selected 15 target genomes.
[2024-01-24 13:42:01,620] [INFO] Target genome list was writen to GCF_004802635.2_ASM480263v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:01,732] [INFO] Task started: fastANI
[2024-01-24 13:42:01,732] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a177eb-e64d-484e-b419-9cd80e42fa5f/GCF_004802635.2_ASM480263v2_genomic.fna.gz --refList GCF_004802635.2_ASM480263v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004802635.2_ASM480263v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:15,005] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:15,019] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:15,020] [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_004802635.2	s__Methylocystis heyeri	100.0	1573	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002862095.1	s__Methylocystis sp002862095	80.3288	644	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745395.1	s__Methylocystis sp016745395	79.1208	486	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003152255.1	s__Methylocystis sp003152255	79.0735	530	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134075.1	s__Methylocystis sp003134075	79.0619	536	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	99.45	99.32	0.87	0.85	6	-
GCF_011058845.1	s__Methylocystis sp011058845	78.8862	491	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000188155.2	s__Methylocystis sp000188155	78.8222	506	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009936375.1	s__Methylosinus sp009936375	78.815	513	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752655.1	s__Methylosinus trichosporium	78.8133	558	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.98	99.98	1.00	1.00	3	-
GCF_000304315.1	s__Methylocystis sp000304315	78.7196	410	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685825.1	s__Methylosinus sp000685825	78.7141	509	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.04	98.49	0.94	0.91	4	-
GCA_002929055.1	s__Methylocystis sp002929055	78.6953	402	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105285.1	s__Methylosinus sp003105285	78.509	401	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869435.1	s__Methylocystis sp016869435	78.3404	361	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315135.1	s__Roseiarcus fermentans	76.9174	309	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Roseiarcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:15,023] [INFO] GTDB search result was written to GCF_004802635.2_ASM480263v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:15,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:15,027] [INFO] DFAST_QC result json was written to GCF_004802635.2_ASM480263v2_genomic.fna/dqc_result.json
[2024-01-24 13:42:15,028] [INFO] DFAST_QC completed!
[2024-01-24 13:42:15,028] [INFO] Total running time: 0h1m29s