[2024-01-24 11:51:50,647] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:50,649] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:50,649] [INFO] DQC Reference Directory: /var/lib/cwl/stg3920f137-ef2d-43ca-ba83-b3cf1b298ef9/dqc_reference
[2024-01-24 11:51:51,833] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,834] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b588bd7-041a-4922-a4b5-b861d63d7717/GCF_003261235.1_ASM326123v1_genomic.fna.gz | prodigal -d GCF_003261235.1_ASM326123v1_genomic.fna/cds.fna -a GCF_003261235.1_ASM326123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:56,488] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:56,489] [INFO] Task started: HMMsearch
[2024-01-24 11:51:56,489] [INFO] Running command: hmmsearch --tblout GCF_003261235.1_ASM326123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3920f137-ef2d-43ca-ba83-b3cf1b298ef9/dqc_reference/reference_markers.hmm GCF_003261235.1_ASM326123v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:56,718] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:56,720] [INFO] Found 6/6 markers.
[2024-01-24 11:51:56,741] [INFO] Query marker FASTA was written to GCF_003261235.1_ASM326123v1_genomic.fna/markers.fasta
[2024-01-24 11:51:56,741] [INFO] Task started: Blastn
[2024-01-24 11:51:56,741] [INFO] Running command: blastn -query GCF_003261235.1_ASM326123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3920f137-ef2d-43ca-ba83-b3cf1b298ef9/dqc_reference/reference_markers.fasta -out GCF_003261235.1_ASM326123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:57,324] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:57,328] [INFO] Selected 14 target genomes.
[2024-01-24 11:51:57,329] [INFO] Target genome list was writen to GCF_003261235.1_ASM326123v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:57,372] [INFO] Task started: fastANI
[2024-01-24 11:51:57,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b588bd7-041a-4922-a4b5-b861d63d7717/GCF_003261235.1_ASM326123v1_genomic.fna.gz --refList GCF_003261235.1_ASM326123v1_genomic.fna/target_genomes.txt --output GCF_003261235.1_ASM326123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:03,000] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:03,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3920f137-ef2d-43ca-ba83-b3cf1b298ef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:03,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3920f137-ef2d-43ca-ba83-b3cf1b298ef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:03,018] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:03,018] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:03,018] [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
Polynucleobacter paneuropaeus	strain=MG-25-Pas1-D2	GCA_003261235.1	2527775	2527775	type	True	100.0	611	611	95	conclusive
Polynucleobacter paludilacus	strain=MWH-Mekk-C3	GCA_018687595.1	1855895	1855895	type	True	86.1131	487	611	95	below_threshold
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	79.6454	230	611	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	79.4316	228	611	95	below_threshold
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	79.4224	205	611	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	79.4088	229	611	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	79.3652	254	611	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	79.3358	235	611	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	79.2829	232	611	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	79.2631	221	611	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	79.1812	232	611	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	79.1784	233	611	95	below_threshold
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	78.9525	206	611	95	below_threshold
Polynucleobacter antarcticus	strain=LimPoW16	GCA_013307245.1	1743162	1743162	type	True	78.8688	201	611	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:03,020] [INFO] DFAST Taxonomy check result was written to GCF_003261235.1_ASM326123v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:03,020] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:03,020] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:03,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3920f137-ef2d-43ca-ba83-b3cf1b298ef9/dqc_reference/checkm_data
[2024-01-24 11:52:03,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:03,041] [INFO] Task started: CheckM
[2024-01-24 11:52:03,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003261235.1_ASM326123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003261235.1_ASM326123v1_genomic.fna/checkm_input GCF_003261235.1_ASM326123v1_genomic.fna/checkm_result
[2024-01-24 11:52:24,014] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:24,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:24,035] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:24,035] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:24,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003261235.1_ASM326123v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:24,036] [INFO] Task started: Blastn
[2024-01-24 11:52:24,036] [INFO] Running command: blastn -query GCF_003261235.1_ASM326123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3920f137-ef2d-43ca-ba83-b3cf1b298ef9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003261235.1_ASM326123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:24,842] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:24,845] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:24,845] [INFO] Target genome list was writen to GCF_003261235.1_ASM326123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:24,876] [INFO] Task started: fastANI
[2024-01-24 11:52:24,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b588bd7-041a-4922-a4b5-b861d63d7717/GCF_003261235.1_ASM326123v1_genomic.fna.gz --refList GCF_003261235.1_ASM326123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003261235.1_ASM326123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:31,684] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:31,701] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:31,701] [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_003261235.1	s__Polynucleobacter paneuropaeus	100.0	611	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.74	98.42	0.90	0.83	33	conclusive
GCF_018687595.1	s__Polynucleobacter asymbioticus_B	86.1029	488	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687555.1	s__Polynucleobacter sp018687555	84.631	455	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.44	97.44	0.90	0.90	2	-
GCF_018687815.1	s__Polynucleobacter sp018687815	79.7241	224	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881855.1	s__Polynucleobacter sp018881855	79.5538	237	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882085.1	s__Polynucleobacter sp018882085	79.4774	231	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192535.1	s__Polynucleobacter hirudinilacicola	79.3869	230	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882155.1	s__Polynucleobacter sp018882155	79.3807	253	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881605.1	s__Polynucleobacter sp018881605	79.3132	231	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881655.1	s__Polynucleobacter sp001889925	79.3079	227	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	96.71	95.84	0.78	0.66	4	-
GCF_018882295.1	s__Polynucleobacter sp018882295	79.2962	239	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882445.1	s__Polynucleobacter sp018882445	79.2472	227	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687455.1	s__Polynucleobacter sp001870365	79.1872	232	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	96.21	96.15	0.92	0.92	3	-
GCF_900095215.1	s__Polynucleobacter necessarius_H	79.1058	194	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900095165.1	s__Polynucleobacter necessarius_J	79.0568	218	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205155.1	s__Polynucleobacter sp013205155	78.6131	148	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903827075.1	s__Polynucleobacter sp903827075	78.2561	178	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.03	0.84	0.82	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:31,703] [INFO] GTDB search result was written to GCF_003261235.1_ASM326123v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:31,703] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:31,708] [INFO] DFAST_QC result json was written to GCF_003261235.1_ASM326123v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:31,708] [INFO] DFAST_QC completed!
[2024-01-24 11:52:31,708] [INFO] Total running time: 0h0m41s