[2024-01-24 14:06:30,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bed45dc-80bc-4a8a-a32f-81e501cca0d9/dqc_reference
[2024-01-24 14:06:31,892] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,893] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,893] [INFO] Running command: gunzip -c /var/lib/cwl/stg96f69adc-b843-4282-8f3f-a2d0daedee32/GCF_007748075.1_ASM774807v1_genomic.fna.gz | prodigal -d GCF_007748075.1_ASM774807v1_genomic.fna/cds.fna -a GCF_007748075.1_ASM774807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:42,582] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:42,582] [INFO] Task started: HMMsearch
[2024-01-24 14:06:42,582] [INFO] Running command: hmmsearch --tblout GCF_007748075.1_ASM774807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bed45dc-80bc-4a8a-a32f-81e501cca0d9/dqc_reference/reference_markers.hmm GCF_007748075.1_ASM774807v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:42,900] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:42,902] [INFO] Found 6/6 markers.
[2024-01-24 14:06:42,942] [INFO] Query marker FASTA was written to GCF_007748075.1_ASM774807v1_genomic.fna/markers.fasta
[2024-01-24 14:06:42,943] [INFO] Task started: Blastn
[2024-01-24 14:06:42,943] [INFO] Running command: blastn -query GCF_007748075.1_ASM774807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bed45dc-80bc-4a8a-a32f-81e501cca0d9/dqc_reference/reference_markers.fasta -out GCF_007748075.1_ASM774807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:43,679] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:43,684] [INFO] Selected 23 target genomes.
[2024-01-24 14:06:43,684] [INFO] Target genome list was writen to GCF_007748075.1_ASM774807v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:43,822] [INFO] Task started: fastANI
[2024-01-24 14:06:43,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg96f69adc-b843-4282-8f3f-a2d0daedee32/GCF_007748075.1_ASM774807v1_genomic.fna.gz --refList GCF_007748075.1_ASM774807v1_genomic.fna/target_genomes.txt --output GCF_007748075.1_ASM774807v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:00,760] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:00,761] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bed45dc-80bc-4a8a-a32f-81e501cca0d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:00,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bed45dc-80bc-4a8a-a32f-81e501cca0d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:00,772] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:00,772] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:00,772] [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
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	100.0	1162	1162	95	conclusive
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	77.0339	152	1162	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	76.6911	141	1162	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	76.6009	138	1162	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.4354	69	1162	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	75.4056	71	1162	95	below_threshold
Streptomonospora alba	strain=YIM 90003	GCA_000826685.1	183763	183763	type	True	74.9258	56	1162	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	74.8977	57	1162	95	below_threshold
Klenkia taihuensis	strain=CGMCC 1.12303	GCA_014653095.1	1225127	1225127	type	True	74.8171	69	1162	95	below_threshold
Klenkia taihuensis	strain=DSM 45962	GCA_900112525.1	1225127	1225127	type	True	74.8148	69	1162	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	74.7708	76	1162	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	74.7443	55	1162	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:00,774] [INFO] DFAST Taxonomy check result was written to GCF_007748075.1_ASM774807v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:00,774] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:00,775] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:00,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bed45dc-80bc-4a8a-a32f-81e501cca0d9/dqc_reference/checkm_data
[2024-01-24 14:07:00,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:00,813] [INFO] Task started: CheckM
[2024-01-24 14:07:00,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007748075.1_ASM774807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007748075.1_ASM774807v1_genomic.fna/checkm_input GCF_007748075.1_ASM774807v1_genomic.fna/checkm_result
[2024-01-24 14:07:40,252] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:40,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:40,272] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:40,272] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:40,273] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007748075.1_ASM774807v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:40,273] [INFO] Task started: Blastn
[2024-01-24 14:07:40,273] [INFO] Running command: blastn -query GCF_007748075.1_ASM774807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bed45dc-80bc-4a8a-a32f-81e501cca0d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_007748075.1_ASM774807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:41,253] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:41,257] [INFO] Selected 20 target genomes.
[2024-01-24 14:07:41,257] [INFO] Target genome list was writen to GCF_007748075.1_ASM774807v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:41,276] [INFO] Task started: fastANI
[2024-01-24 14:07:41,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg96f69adc-b843-4282-8f3f-a2d0daedee32/GCF_007748075.1_ASM774807v1_genomic.fna.gz --refList GCF_007748075.1_ASM774807v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007748075.1_ASM774807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:56,405] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:56,423] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:56,423] [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
GCA_007748075.1	s__Pan265 sp007748075	100.0	1162	1162	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Pan265	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014207595.1	s__Algisphaera agarilytica	77.0669	150	1162	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Algisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284115.1	s__Phycisphaera mikurensis	76.7066	140	1162	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Phycisphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016125215.1	s__RI-382 sp016125215	76.702	141	1162	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__RI-382	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696675.1	s__UBA6054 sp003696675	76.5665	70	1162	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551485.1	s__B1Sed10-187 sp003551485	76.2819	79	1162	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__B1Sed10-187	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693765.1	s__RECZ01 sp007693765	76.2323	91	1162	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686995.1	s__GCA-2686995 sp002686995	76.0154	105	1162	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__GCA-2686995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119405.1	s__SKPT01 sp007119405	75.9451	84	1162	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__SKPT01	95.0	98.45	98.45	0.84	0.84	2	-
GCF_009765365.1	s__VTOM01 sp009765365	75.4061	52	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VTOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959175.1	s__CAJBVW01 sp903959175	74.9841	62	1162	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAJBVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170275.1	s__PALSA-1104 sp003170275	74.6477	52	1162	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__Palsa-1104;g__PALSA-1104	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:56,425] [INFO] GTDB search result was written to GCF_007748075.1_ASM774807v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:56,425] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:56,428] [INFO] DFAST_QC result json was written to GCF_007748075.1_ASM774807v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:56,429] [INFO] DFAST_QC completed!
[2024-01-24 14:07:56,429] [INFO] Total running time: 0h1m26s