[2024-01-24 10:58:06,472] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,475] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4133861-a3f1-4a6f-bbeb-abced2d2a478/dqc_reference
[2024-01-24 10:58:09,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,635] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg271ed4cb-318d-4d65-8b11-43fc9802036b/GCF_010435925.1_ASM1043592v1_genomic.fna.gz | prodigal -d GCF_010435925.1_ASM1043592v1_genomic.fna/cds.fna -a GCF_010435925.1_ASM1043592v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:20,341] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:20,342] [INFO] Task started: HMMsearch
[2024-01-24 10:58:20,342] [INFO] Running command: hmmsearch --tblout GCF_010435925.1_ASM1043592v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4133861-a3f1-4a6f-bbeb-abced2d2a478/dqc_reference/reference_markers.hmm GCF_010435925.1_ASM1043592v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:20,629] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:20,630] [INFO] Found 6/6 markers.
[2024-01-24 10:58:20,666] [INFO] Query marker FASTA was written to GCF_010435925.1_ASM1043592v1_genomic.fna/markers.fasta
[2024-01-24 10:58:20,667] [INFO] Task started: Blastn
[2024-01-24 10:58:20,667] [INFO] Running command: blastn -query GCF_010435925.1_ASM1043592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4133861-a3f1-4a6f-bbeb-abced2d2a478/dqc_reference/reference_markers.fasta -out GCF_010435925.1_ASM1043592v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:21,648] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:21,652] [INFO] Selected 20 target genomes.
[2024-01-24 10:58:21,652] [INFO] Target genome list was writen to GCF_010435925.1_ASM1043592v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:21,661] [INFO] Task started: fastANI
[2024-01-24 10:58:21,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg271ed4cb-318d-4d65-8b11-43fc9802036b/GCF_010435925.1_ASM1043592v1_genomic.fna.gz --refList GCF_010435925.1_ASM1043592v1_genomic.fna/target_genomes.txt --output GCF_010435925.1_ASM1043592v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:37,930] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:37,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4133861-a3f1-4a6f-bbeb-abced2d2a478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:37,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4133861-a3f1-4a6f-bbeb-abced2d2a478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:37,951] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:37,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:37,952] [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
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_012070395.1	2705421	2705421	type	True	100.0	1280	1281	95	conclusive
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	100.0	1280	1281	95	conclusive
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	79.8938	656	1281	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	79.8691	662	1281	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	79.8449	661	1281	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.6149	593	1281	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	79.4182	599	1281	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	79.1891	494	1281	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	79.1064	487	1281	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.9392	495	1281	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.582	474	1281	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	78.4737	401	1281	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.4509	394	1281	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	78.2709	510	1281	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.2646	513	1281	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.7463	311	1281	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.6366	298	1281	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.5814	340	1281	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.1851	260	1281	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.9227	240	1281	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:37,953] [INFO] DFAST Taxonomy check result was written to GCF_010435925.1_ASM1043592v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:37,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:37,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:37,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4133861-a3f1-4a6f-bbeb-abced2d2a478/dqc_reference/checkm_data
[2024-01-24 10:58:37,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:37,992] [INFO] Task started: CheckM
[2024-01-24 10:58:37,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010435925.1_ASM1043592v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010435925.1_ASM1043592v1_genomic.fna/checkm_input GCF_010435925.1_ASM1043592v1_genomic.fna/checkm_result
[2024-01-24 10:59:13,749] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:13,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:13,775] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:13,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:13,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010435925.1_ASM1043592v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:13,776] [INFO] Task started: Blastn
[2024-01-24 10:59:13,776] [INFO] Running command: blastn -query GCF_010435925.1_ASM1043592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4133861-a3f1-4a6f-bbeb-abced2d2a478/dqc_reference/reference_markers_gtdb.fasta -out GCF_010435925.1_ASM1043592v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:15,673] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:15,677] [INFO] Selected 20 target genomes.
[2024-01-24 10:59:15,678] [INFO] Target genome list was writen to GCF_010435925.1_ASM1043592v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:15,693] [INFO] Task started: fastANI
[2024-01-24 10:59:15,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg271ed4cb-318d-4d65-8b11-43fc9802036b/GCF_010435925.1_ASM1043592v1_genomic.fna.gz --refList GCF_010435925.1_ASM1043592v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010435925.1_ASM1043592v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:32,143] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:32,167] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:32,168] [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_012070395.1	s__CLL3-39 sp012070395	100.0	1280	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CLL3-39	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000379485.1	s__Wenxinia marina	79.8242	664	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.6595	587	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	79.4593	594	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	79.3439	513	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	79.1697	496	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900172345.1	s__Limimaricola soesokkakensis	78.9554	498	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000521865.1	s__Roseivivax isoporae	78.5476	478	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	78.495	394	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521785.1	s__Roseivivax halodurans	78.4537	403	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	78.4337	494	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCA_011620265.1	s__Albidovulum sp011620265	78.4126	412	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223355.1	s__Salipiger pacificus_B	78.3824	519	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	78.3491	468	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689705.1	s__HKCCE3408 sp015689705	78.1976	417	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102905.1	s__Meinhardsimonia xiamenensis	78.1404	400	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Meinhardsimonia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002166865.1	s__Roseovarius sp002166865	78.0037	348	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000435.1	s__Flavimaricola sp004000435	77.7358	312	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	99.99	99.97	0.99	0.98	36	-
GCF_016428585.1	s__Sedimentitalea sp016428585	77.6686	297	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172255.1	s__Roseovarius halotolerans	77.6131	303	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:32,170] [INFO] GTDB search result was written to GCF_010435925.1_ASM1043592v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:32,170] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:32,175] [INFO] DFAST_QC result json was written to GCF_010435925.1_ASM1043592v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:32,175] [INFO] DFAST_QC completed!
[2024-01-24 10:59:32,176] [INFO] Total running time: 0h1m26s