[2023-06-30 15:08:56,916] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:08:56,918] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:08:56,918] [INFO] DQC Reference Directory: /var/lib/cwl/stg94d9793a-df5a-4f04-8d6b-1e4c1722afe3/dqc_reference
[2023-06-30 15:08:58,931] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:08:58,932] [INFO] Task started: Prodigal
[2023-06-30 15:08:58,932] [INFO] Running command: gunzip -c /var/lib/cwl/stg9547e1b2-0815-4c3c-b615-8bffe1790587/GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna.gz | prodigal -d GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/cds.fna -a GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:09:03,371] [INFO] Task succeeded: Prodigal
[2023-06-30 15:09:03,371] [INFO] Task started: HMMsearch
[2023-06-30 15:09:03,372] [INFO] Running command: hmmsearch --tblout GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94d9793a-df5a-4f04-8d6b-1e4c1722afe3/dqc_reference/reference_markers.hmm GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:09:03,618] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:09:03,620] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9547e1b2-0815-4c3c-b615-8bffe1790587/GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna.gz]
[2023-06-30 15:09:03,641] [INFO] Query marker FASTA was written to GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/markers.fasta
[2023-06-30 15:09:03,642] [INFO] Task started: Blastn
[2023-06-30 15:09:03,642] [INFO] Running command: blastn -query GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/markers.fasta -db /var/lib/cwl/stg94d9793a-df5a-4f04-8d6b-1e4c1722afe3/dqc_reference/reference_markers.fasta -out GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:09:04,257] [INFO] Task succeeded: Blastn
[2023-06-30 15:09:04,261] [INFO] Selected 14 target genomes.
[2023-06-30 15:09:04,261] [INFO] Target genome list was writen to GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/target_genomes.txt
[2023-06-30 15:09:04,263] [INFO] Task started: fastANI
[2023-06-30 15:09:04,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg9547e1b2-0815-4c3c-b615-8bffe1790587/GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna.gz --refList GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/target_genomes.txt --output GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:09:12,255] [INFO] Task succeeded: fastANI
[2023-06-30 15:09:12,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94d9793a-df5a-4f04-8d6b-1e4c1722afe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:09:12,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94d9793a-df5a-4f04-8d6b-1e4c1722afe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:09:12,264] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:09:12,264] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:09:12,264] [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
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	82.4993	373	528	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	78.6641	230	528	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	78.3267	108	528	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	77.1147	107	528	95	below_threshold
Pelodictyon luteolum	strain=DSM 273	GCA_000012485.1	1100	1100	type	True	76.8256	72	528	95	below_threshold
Chlorobaculum limnaeum	strain=DSM 1677	GCA_001747405.1	274537	274537	type	True	76.412	56	528	95	below_threshold
Chlorobaculum thiosulfatiphilum	strain=DSM 249	GCA_006265165.1	115852	115852	type	True	76.1852	58	528	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:09:12,266] [INFO] DFAST Taxonomy check result was written to GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/tc_result.tsv
[2023-06-30 15:09:12,267] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:09:12,267] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:09:12,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94d9793a-df5a-4f04-8d6b-1e4c1722afe3/dqc_reference/checkm_data
[2023-06-30 15:09:12,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:09:12,291] [INFO] Task started: CheckM
[2023-06-30 15:09:12,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/checkm_input GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/checkm_result
[2023-06-30 15:09:40,080] [INFO] Task succeeded: CheckM
[2023-06-30 15:09:40,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:09:40,099] [INFO] ===== Completeness check finished =====
[2023-06-30 15:09:40,099] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:09:40,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/markers.fasta)
[2023-06-30 15:09:40,100] [INFO] Task started: Blastn
[2023-06-30 15:09:40,100] [INFO] Running command: blastn -query GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/markers.fasta -db /var/lib/cwl/stg94d9793a-df5a-4f04-8d6b-1e4c1722afe3/dqc_reference/reference_markers_gtdb.fasta -out GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:09:40,963] [INFO] Task succeeded: Blastn
[2023-06-30 15:09:40,967] [INFO] Selected 11 target genomes.
[2023-06-30 15:09:40,968] [INFO] Target genome list was writen to GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:09:40,969] [INFO] Task started: fastANI
[2023-06-30 15:09:40,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg9547e1b2-0815-4c3c-b615-8bffe1790587/GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna.gz --refList GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/target_genomes_gtdb.txt --output GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:09:46,666] [INFO] Task succeeded: fastANI
[2023-06-30 15:09:46,681] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:09:46,682] [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
GCA_903820085.1	s__Chlorobium sp903820085	99.997	527	528	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.98	99.89	0.98	0.91	15	conclusive
GCA_903942355.1	s__Chlorobium sp903942355	90.4259	307	528	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.73	99.73	0.79	0.79	2	-
GCA_903865705.1	s__Chlorobium sp903865705	86.2832	378	528	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.47	99.06	0.91	0.87	5	-
GCA_903822595.1	s__Chlorobium sp903822595	83.5486	402	528	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.84	99.77	0.94	0.93	3	-
GCA_903882665.1	s__Chlorobium sp903882665	83.5301	399	528	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.16	98.83	0.90	0.84	7	-
GCA_903939765.1	s__Chlorobium sp903939765	82.9355	389	528	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.90	99.86	0.94	0.94	3	-
GCF_000020645.1	s__Chlorobium phaeoclathratiforme	82.4993	373	528	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_903824295.1	s__Chlorobium sp903824295	82.479	385	528	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.79	99.65	0.92	0.89	3	-
GCA_013334755.1	s__Chlorobium sp013334755	82.0532	325	528	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.60	99.60	0.88	0.88	2	-
GCA_903937835.1	s__Chlorobium sp903937835	80.247	276	528	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.77	99.60	0.93	0.86	6	-
GCA_903887845.1	s__Chlorobium sp903887845	79.8989	293	528	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.96	99.96	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-30 15:09:46,684] [INFO] GTDB search result was written to GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/result_gtdb.tsv
[2023-06-30 15:09:46,684] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:09:46,687] [INFO] DFAST_QC result json was written to GCA_903883565.1_freshwater_MAG_---_D4_bin-019_genomic.fna/dqc_result.json
[2023-06-30 15:09:46,688] [INFO] DFAST_QC completed!
[2023-06-30 15:09:46,688] [INFO] Total running time: 0h0m50s