[2024-01-24 13:36:45,200] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg68d16b39-eb21-4f9a-815c-ac95ee4c9320/dqc_reference
[2024-01-24 13:36:46,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,589] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,590] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7cc9aac-d1f3-4ba8-9268-5104a21db9ed/GCF_009177095.1_ASM917709v1_genomic.fna.gz | prodigal -d GCF_009177095.1_ASM917709v1_genomic.fna/cds.fna -a GCF_009177095.1_ASM917709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:09,220] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:09,220] [INFO] Task started: HMMsearch
[2024-01-24 13:37:09,220] [INFO] Running command: hmmsearch --tblout GCF_009177095.1_ASM917709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68d16b39-eb21-4f9a-815c-ac95ee4c9320/dqc_reference/reference_markers.hmm GCF_009177095.1_ASM917709v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:09,558] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:09,559] [INFO] Found 6/6 markers.
[2024-01-24 13:37:09,612] [INFO] Query marker FASTA was written to GCF_009177095.1_ASM917709v1_genomic.fna/markers.fasta
[2024-01-24 13:37:09,613] [INFO] Task started: Blastn
[2024-01-24 13:37:09,613] [INFO] Running command: blastn -query GCF_009177095.1_ASM917709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68d16b39-eb21-4f9a-815c-ac95ee4c9320/dqc_reference/reference_markers.fasta -out GCF_009177095.1_ASM917709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:10,273] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:10,276] [INFO] Selected 19 target genomes.
[2024-01-24 13:37:10,277] [INFO] Target genome list was writen to GCF_009177095.1_ASM917709v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:10,291] [INFO] Task started: fastANI
[2024-01-24 13:37:10,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7cc9aac-d1f3-4ba8-9268-5104a21db9ed/GCF_009177095.1_ASM917709v1_genomic.fna.gz --refList GCF_009177095.1_ASM917709v1_genomic.fna/target_genomes.txt --output GCF_009177095.1_ASM917709v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:29,663] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:29,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68d16b39-eb21-4f9a-815c-ac95ee4c9320/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:29,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68d16b39-eb21-4f9a-815c-ac95ee4c9320/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:29,676] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:29,676] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:29,676] [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
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	100.0	2307	2307	95	conclusive
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	81.0662	1092	2307	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	77.0207	281	2307	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.8989	292	2307	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	76.7821	290	2307	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	76.7691	295	2307	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.6624	272	2307	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	76.5674	283	2307	95	below_threshold
Bythopirellula polymerisocia	strain=Pla144	GCA_007860015.1	2528003	2528003	type	True	76.4505	82	2307	95	below_threshold
Adhaeretor mobilis	strain=HG15A2	GCA_007741515.1	1930276	1930276	type	True	75.9326	122	2307	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.8487	122	2307	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	75.8127	51	2307	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.454	157	2307	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	74.6447	68	2307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:29,678] [INFO] DFAST Taxonomy check result was written to GCF_009177095.1_ASM917709v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:29,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:29,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:29,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68d16b39-eb21-4f9a-815c-ac95ee4c9320/dqc_reference/checkm_data
[2024-01-24 13:37:29,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:29,749] [INFO] Task started: CheckM
[2024-01-24 13:37:29,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009177095.1_ASM917709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009177095.1_ASM917709v1_genomic.fna/checkm_input GCF_009177095.1_ASM917709v1_genomic.fna/checkm_result
[2024-01-24 13:38:30,568] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:30,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:30,587] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:30,588] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:30,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009177095.1_ASM917709v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:30,588] [INFO] Task started: Blastn
[2024-01-24 13:38:30,588] [INFO] Running command: blastn -query GCF_009177095.1_ASM917709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68d16b39-eb21-4f9a-815c-ac95ee4c9320/dqc_reference/reference_markers_gtdb.fasta -out GCF_009177095.1_ASM917709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:31,412] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:31,415] [INFO] Selected 17 target genomes.
[2024-01-24 13:38:31,415] [INFO] Target genome list was writen to GCF_009177095.1_ASM917709v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:31,435] [INFO] Task started: fastANI
[2024-01-24 13:38:31,435] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7cc9aac-d1f3-4ba8-9268-5104a21db9ed/GCF_009177095.1_ASM917709v1_genomic.fna.gz --refList GCF_009177095.1_ASM917709v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009177095.1_ASM917709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:49,106] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:49,118] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:49,118] [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_009177095.1	s__Lacipirellula parvula	100.0	2307	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013822725.1	s__Lacipirellula sp013822725	82.2752	1003	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007746075.1	s__Lacipirellula limnantheis	81.0505	1095	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	97.19	97.19	0.90	0.90	2	-
GCA_003576855.1	s__Lacipirellula sp003576855	77.4868	462	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	77.0841	397	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007753265.1	s__Botrimarina mediterranea	77.0308	280	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	99.49	99.49	0.94	0.94	2	-
GCF_007859945.1	s__Pseudobythopirellula maris	76.8911	294	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	76.792	292	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859955.1	s__Botrimarina colliarenosi	76.752	293	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007748035.1	s__Aeoliella mucimassa	76.2456	160	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Aeoliella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191115.1	s__JACPPG01 sp016191115	76.1269	139	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JACPPG01;g__JACPPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152205.1	s__Bythopirellula sp013152205	76.1059	82	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064595.1	s__Paludisphaera soli	75.4315	161	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778405.1	s__SXOA01 sp005778405	75.1191	75	2307	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__SXOA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:49,120] [INFO] GTDB search result was written to GCF_009177095.1_ASM917709v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:49,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:49,124] [INFO] DFAST_QC result json was written to GCF_009177095.1_ASM917709v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:49,124] [INFO] DFAST_QC completed!
[2024-01-24 13:38:49,124] [INFO] Total running time: 0h2m4s