[2024-01-24 14:11:46,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,285] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d539130-8f3f-449d-a428-585ba4c2b095/dqc_reference
[2024-01-24 14:11:48,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:48,879] [INFO] Task started: Prodigal
[2024-01-24 14:11:48,879] [INFO] Running command: gunzip -c /var/lib/cwl/stge20e953e-90d4-49ca-ab92-40ec29836b3b/GCF_008374075.1_ASM837407v1_genomic.fna.gz | prodigal -d GCF_008374075.1_ASM837407v1_genomic.fna/cds.fna -a GCF_008374075.1_ASM837407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:18,596] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:18,597] [INFO] Task started: HMMsearch
[2024-01-24 14:12:18,597] [INFO] Running command: hmmsearch --tblout GCF_008374075.1_ASM837407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d539130-8f3f-449d-a428-585ba4c2b095/dqc_reference/reference_markers.hmm GCF_008374075.1_ASM837407v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:19,004] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:19,006] [INFO] Found 6/6 markers.
[2024-01-24 14:12:19,093] [INFO] Query marker FASTA was written to GCF_008374075.1_ASM837407v1_genomic.fna/markers.fasta
[2024-01-24 14:12:19,094] [INFO] Task started: Blastn
[2024-01-24 14:12:19,094] [INFO] Running command: blastn -query GCF_008374075.1_ASM837407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d539130-8f3f-449d-a428-585ba4c2b095/dqc_reference/reference_markers.fasta -out GCF_008374075.1_ASM837407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:19,790] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:19,794] [INFO] Selected 18 target genomes.
[2024-01-24 14:12:19,795] [INFO] Target genome list was writen to GCF_008374075.1_ASM837407v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:19,803] [INFO] Task started: fastANI
[2024-01-24 14:12:19,803] [INFO] Running command: fastANI --query /var/lib/cwl/stge20e953e-90d4-49ca-ab92-40ec29836b3b/GCF_008374075.1_ASM837407v1_genomic.fna.gz --refList GCF_008374075.1_ASM837407v1_genomic.fna/target_genomes.txt --output GCF_008374075.1_ASM837407v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:59,990] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:59,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d539130-8f3f-449d-a428-585ba4c2b095/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:59,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d539130-8f3f-449d-a428-585ba4c2b095/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:00,007] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:13:00,007] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:00,007] [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
Rubripirellula obstinata	strain=LF1	GCA_008374075.1	406547	406547	type	True	100.0	2348	2350	95	conclusive
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	99.8492	2022	2350	95	conclusive
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	78.1843	224	2350	95	below_threshold
Rubripirellula amarantea	strain=Pla22	GCA_007859865.1	2527999	2527999	type	True	78.0145	277	2350	95	below_threshold
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	77.7266	321	2350	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	77.309	285	2350	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	77.2872	199	2350	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	77.2164	321	2350	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	76.9107	198	2350	95	below_threshold
Novipirellula artificiosorum	strain=Poly41	GCA_007860135.1	2528016	2528016	type	True	76.779	161	2350	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	76.7428	195	2350	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	76.7024	175	2350	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	76.5977	179	2350	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	76.1757	115	2350	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:00,009] [INFO] DFAST Taxonomy check result was written to GCF_008374075.1_ASM837407v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:00,009] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:00,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:00,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d539130-8f3f-449d-a428-585ba4c2b095/dqc_reference/checkm_data
[2024-01-24 14:13:00,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:00,085] [INFO] Task started: CheckM
[2024-01-24 14:13:00,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008374075.1_ASM837407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008374075.1_ASM837407v1_genomic.fna/checkm_input GCF_008374075.1_ASM837407v1_genomic.fna/checkm_result
[2024-01-24 14:14:26,633] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:26,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:26,661] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:26,662] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:26,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008374075.1_ASM837407v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:26,663] [INFO] Task started: Blastn
[2024-01-24 14:14:26,664] [INFO] Running command: blastn -query GCF_008374075.1_ASM837407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d539130-8f3f-449d-a428-585ba4c2b095/dqc_reference/reference_markers_gtdb.fasta -out GCF_008374075.1_ASM837407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:29,417] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:29,422] [INFO] Selected 19 target genomes.
[2024-01-24 14:14:29,422] [INFO] Target genome list was writen to GCF_008374075.1_ASM837407v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:29,448] [INFO] Task started: fastANI
[2024-01-24 14:14:29,448] [INFO] Running command: fastANI --query /var/lib/cwl/stge20e953e-90d4-49ca-ab92-40ec29836b3b/GCF_008374075.1_ASM837407v1_genomic.fna.gz --refList GCF_008374075.1_ASM837407v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008374075.1_ASM837407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:08,067] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:08,120] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:08,121] [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_001642955.1	s__Rubripirellula obstinata	99.8492	2022	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	99.93	99.93	1.00	1.00	2	conclusive
GCF_014192335.1	s__Rhodopirellula rubra	78.2043	222	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCF_007859865.1	s__Rubripirellula amarantea	78.0276	275	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860125.1	s__Rubripirellula tenax	77.7245	323	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860175.1	s__Rubripirellula reticaptiva	77.3034	285	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741535.1	s__Rubripirellula sp007741535	77.2088	324	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012290005.1	s__Crateriforma spongiae	77.2086	200	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCF_007860185.1	s__Novipirellula aureliae	77.2046	140	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741555.1	s__K23-9 sp007741555	77.0345	209	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__K23-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338295.1	s__Rhodopirellula europaea	76.8979	198	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCF_001027925.1	s__Rhodopirellula islandica	76.7244	198	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196115.1	s__Rhodopirellula baltica	76.7024	175	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	-
GCF_007860045.1	s__Stieleria varia	76.6096	178	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007753675.1	s__Stieleria sp007753675	76.5884	222	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008035925.1	s__Stieleria maiorica	76.3813	208	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754155.1	s__Stieleria neptunia	76.3034	207	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	76.2718	173	2350	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:08,122] [INFO] GTDB search result was written to GCF_008374075.1_ASM837407v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:08,123] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:08,127] [INFO] DFAST_QC result json was written to GCF_008374075.1_ASM837407v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:08,127] [INFO] DFAST_QC completed!
[2024-01-24 14:15:08,127] [INFO] Total running time: 0h3m22s