[2024-01-24 13:17:04,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:04,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:04,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg239bfd96-66c1-4986-b6fd-f4b5da6d7a13/dqc_reference
[2024-01-24 13:17:05,629] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:05,630] [INFO] Task started: Prodigal
[2024-01-24 13:17:05,630] [INFO] Running command: gunzip -c /var/lib/cwl/stg4989728c-fcb9-45ea-a89c-8d86411ab56b/GCF_003751345.1_ASM375134v1_genomic.fna.gz | prodigal -d GCF_003751345.1_ASM375134v1_genomic.fna/cds.fna -a GCF_003751345.1_ASM375134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:23,432] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:23,432] [INFO] Task started: HMMsearch
[2024-01-24 13:17:23,432] [INFO] Running command: hmmsearch --tblout GCF_003751345.1_ASM375134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg239bfd96-66c1-4986-b6fd-f4b5da6d7a13/dqc_reference/reference_markers.hmm GCF_003751345.1_ASM375134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:23,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:23,789] [INFO] Found 6/6 markers.
[2024-01-24 13:17:23,839] [INFO] Query marker FASTA was written to GCF_003751345.1_ASM375134v1_genomic.fna/markers.fasta
[2024-01-24 13:17:23,840] [INFO] Task started: Blastn
[2024-01-24 13:17:23,840] [INFO] Running command: blastn -query GCF_003751345.1_ASM375134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg239bfd96-66c1-4986-b6fd-f4b5da6d7a13/dqc_reference/reference_markers.fasta -out GCF_003751345.1_ASM375134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:24,851] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:24,855] [INFO] Selected 23 target genomes.
[2024-01-24 13:17:24,856] [INFO] Target genome list was writen to GCF_003751345.1_ASM375134v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:24,871] [INFO] Task started: fastANI
[2024-01-24 13:17:24,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg4989728c-fcb9-45ea-a89c-8d86411ab56b/GCF_003751345.1_ASM375134v1_genomic.fna.gz --refList GCF_003751345.1_ASM375134v1_genomic.fna/target_genomes.txt --output GCF_003751345.1_ASM375134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:52,658] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:52,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg239bfd96-66c1-4986-b6fd-f4b5da6d7a13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:52,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg239bfd96-66c1-4986-b6fd-f4b5da6d7a13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:52,677] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:52,678] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:52,678] [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
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	100.0	1930	1933	95	conclusive
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	99.995	1928	1933	95	conclusive
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.3916	407	1933	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	77.2319	591	1933	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	77.2125	556	1933	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	77.2023	476	1933	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	77.1404	588	1933	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	77.0964	605	1933	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	77.0764	533	1933	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	77.0653	643	1933	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	77.0506	570	1933	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	77.0261	601	1933	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.9878	585	1933	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.9871	429	1933	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	76.9567	582	1933	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.8947	584	1933	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.8592	560	1933	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.8144	381	1933	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.455	444	1933	95	below_threshold
Fodinicurvata fenggangensis	strain=DSM 21160	GCA_000686045.1	1121830	1121830	type	True	76.3753	172	1933	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.3404	466	1933	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.2047	444	1933	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.099	391	1933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:52,680] [INFO] DFAST Taxonomy check result was written to GCF_003751345.1_ASM375134v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:52,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:52,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:52,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg239bfd96-66c1-4986-b6fd-f4b5da6d7a13/dqc_reference/checkm_data
[2024-01-24 13:17:52,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:52,737] [INFO] Task started: CheckM
[2024-01-24 13:17:52,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003751345.1_ASM375134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003751345.1_ASM375134v1_genomic.fna/checkm_input GCF_003751345.1_ASM375134v1_genomic.fna/checkm_result
[2024-01-24 13:18:48,061] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:48,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:48,086] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:48,086] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:48,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003751345.1_ASM375134v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:48,087] [INFO] Task started: Blastn
[2024-01-24 13:18:48,087] [INFO] Running command: blastn -query GCF_003751345.1_ASM375134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg239bfd96-66c1-4986-b6fd-f4b5da6d7a13/dqc_reference/reference_markers_gtdb.fasta -out GCF_003751345.1_ASM375134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:49,949] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:49,953] [INFO] Selected 17 target genomes.
[2024-01-24 13:18:49,953] [INFO] Target genome list was writen to GCF_003751345.1_ASM375134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:49,970] [INFO] Task started: fastANI
[2024-01-24 13:18:49,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg4989728c-fcb9-45ea-a89c-8d86411ab56b/GCF_003751345.1_ASM375134v1_genomic.fna.gz --refList GCF_003751345.1_ASM375134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003751345.1_ASM375134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:10,886] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:10,901] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:10,902] [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_006738645.1	s__Stella humosa	99.995	1928	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_006739055.1	s__Stella vacuolata	85.9587	1513	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	83.6471	1361	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	77.2594	515	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	77.2029	560	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130795.1	s__Azospirillum thermophilum	77.1997	598	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	77.1497	585	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016869645.1	s__SHVW01 sp016869645	77.1338	444	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364795.1	s__Azospirillum oryzae	77.0674	533	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCF_003989665.1	s__Azospirillum doebereinerae	77.0389	571	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	77.0348	529	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	77.0038	427	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429625.1	s__Azospirillum halopraeferens	76.8814	556	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	76.8505	486	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	76.8398	377	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240395.1	s__JAFAYA01 sp019240395	76.371	342	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	76.1923	309	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:10,903] [INFO] GTDB search result was written to GCF_003751345.1_ASM375134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:10,904] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:10,913] [INFO] DFAST_QC result json was written to GCF_003751345.1_ASM375134v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:10,913] [INFO] DFAST_QC completed!
[2024-01-24 13:19:10,913] [INFO] Total running time: 0h2m7s