[2024-01-24 13:27:56,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:56,923] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:56,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg73be81d8-79d4-43c7-8210-b1bf524342a9/dqc_reference
[2024-01-24 13:27:58,164] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:58,168] [INFO] Task started: Prodigal
[2024-01-24 13:27:58,168] [INFO] Running command: gunzip -c /var/lib/cwl/stg0eb8a04b-c376-45c1-b89d-f0c4d65d5e1c/GCF_022227785.1_ASM2222778v1_genomic.fna.gz | prodigal -d GCF_022227785.1_ASM2222778v1_genomic.fna/cds.fna -a GCF_022227785.1_ASM2222778v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:08,143] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:08,143] [INFO] Task started: HMMsearch
[2024-01-24 13:28:08,143] [INFO] Running command: hmmsearch --tblout GCF_022227785.1_ASM2222778v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73be81d8-79d4-43c7-8210-b1bf524342a9/dqc_reference/reference_markers.hmm GCF_022227785.1_ASM2222778v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:08,436] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:08,437] [INFO] Found 6/6 markers.
[2024-01-24 13:28:08,463] [INFO] Query marker FASTA was written to GCF_022227785.1_ASM2222778v1_genomic.fna/markers.fasta
[2024-01-24 13:28:08,463] [INFO] Task started: Blastn
[2024-01-24 13:28:08,463] [INFO] Running command: blastn -query GCF_022227785.1_ASM2222778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73be81d8-79d4-43c7-8210-b1bf524342a9/dqc_reference/reference_markers.fasta -out GCF_022227785.1_ASM2222778v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:09,263] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:09,309] [INFO] Selected 19 target genomes.
[2024-01-24 13:28:09,310] [INFO] Target genome list was writen to GCF_022227785.1_ASM2222778v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:09,331] [INFO] Task started: fastANI
[2024-01-24 13:28:09,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg0eb8a04b-c376-45c1-b89d-f0c4d65d5e1c/GCF_022227785.1_ASM2222778v1_genomic.fna.gz --refList GCF_022227785.1_ASM2222778v1_genomic.fna/target_genomes.txt --output GCF_022227785.1_ASM2222778v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:22,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:22,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73be81d8-79d4-43c7-8210-b1bf524342a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:22,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73be81d8-79d4-43c7-8210-b1bf524342a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:22,260] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:22,261] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:22,261] [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
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	85.4396	604	1052	95	below_threshold
Ectothiorhodospira marina	strain=DSM 241	GCA_900109495.1	1396821	1396821	type	True	80.0095	522	1052	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	79.5195	399	1052	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	78.4277	299	1052	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	78.3899	282	1052	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.7219	207	1052	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.5387	174	1052	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	77.0999	156	1052	95	below_threshold
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	76.9934	136	1052	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.7942	134	1052	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.7617	143	1052	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	76.5835	141	1052	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	76.5646	113	1052	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	76.5413	101	1052	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	76.5188	166	1052	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	76.513	90	1052	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.0979	93	1052	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	75.9687	92	1052	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	75.9558	107	1052	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:22,262] [INFO] DFAST Taxonomy check result was written to GCF_022227785.1_ASM2222778v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:22,263] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:22,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:22,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73be81d8-79d4-43c7-8210-b1bf524342a9/dqc_reference/checkm_data
[2024-01-24 13:28:22,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:22,299] [INFO] Task started: CheckM
[2024-01-24 13:28:22,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022227785.1_ASM2222778v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022227785.1_ASM2222778v1_genomic.fna/checkm_input GCF_022227785.1_ASM2222778v1_genomic.fna/checkm_result
[2024-01-24 13:28:59,188] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:59,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:59,212] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:59,212] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:59,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022227785.1_ASM2222778v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:59,213] [INFO] Task started: Blastn
[2024-01-24 13:28:59,213] [INFO] Running command: blastn -query GCF_022227785.1_ASM2222778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73be81d8-79d4-43c7-8210-b1bf524342a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_022227785.1_ASM2222778v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:00,571] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:00,574] [INFO] Selected 10 target genomes.
[2024-01-24 13:29:00,574] [INFO] Target genome list was writen to GCF_022227785.1_ASM2222778v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:00,584] [INFO] Task started: fastANI
[2024-01-24 13:29:00,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg0eb8a04b-c376-45c1-b89d-f0c4d65d5e1c/GCF_022227785.1_ASM2222778v1_genomic.fna.gz --refList GCF_022227785.1_ASM2222778v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022227785.1_ASM2222778v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:07,777] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:07,792] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:29:07,792] [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_000225005.1	s__Ectothiorhodospira sp000225005	89.8561	794	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584105.1	s__Ectothiorhodospira shaposhnikovii	89.1732	846	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110965.1	s__Ectothiorhodospira magna	85.4396	604	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632845.1	s__Ectothiorhodospira sp001632845	80.7451	582	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	99.06	99.06	0.98	0.98	2	-
GCF_000633935.1	s__Ectothiorhodospira haloalkaliphila	80.3876	547	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	99.86	99.86	0.97	0.97	2	-
GCF_016584115.1	s__Ectothiorhodospira mobilis	80.3223	457	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114895.1	s__Ectothiorhodospira mobilis_A	80.1821	466	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	79.5451	397	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	79.3932	385	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000365.1	s__Thioalkalivibrio_A denitrificans	78.3899	282	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:07,794] [INFO] GTDB search result was written to GCF_022227785.1_ASM2222778v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:07,795] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:07,798] [INFO] DFAST_QC result json was written to GCF_022227785.1_ASM2222778v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:07,799] [INFO] DFAST_QC completed!
[2024-01-24 13:29:07,799] [INFO] Total running time: 0h1m11s