[2024-01-24 13:27:58,686] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,694] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6d14439-e77f-4af8-887b-1ee8fbf3ce41/dqc_reference
[2024-01-24 13:27:59,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,890] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d36a12b-0414-4144-9898-425175385206/GCF_000330725.2_ASM33072v2_genomic.fna.gz | prodigal -d GCF_000330725.2_ASM33072v2_genomic.fna/cds.fna -a GCF_000330725.2_ASM33072v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:29,703] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:29,704] [INFO] Task started: HMMsearch
[2024-01-24 13:28:29,704] [INFO] Running command: hmmsearch --tblout GCF_000330725.2_ASM33072v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6d14439-e77f-4af8-887b-1ee8fbf3ce41/dqc_reference/reference_markers.hmm GCF_000330725.2_ASM33072v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:30,050] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:30,052] [INFO] Found 6/6 markers.
[2024-01-24 13:28:30,092] [INFO] Query marker FASTA was written to GCF_000330725.2_ASM33072v2_genomic.fna/markers.fasta
[2024-01-24 13:28:30,092] [INFO] Task started: Blastn
[2024-01-24 13:28:30,092] [INFO] Running command: blastn -query GCF_000330725.2_ASM33072v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6d14439-e77f-4af8-887b-1ee8fbf3ce41/dqc_reference/reference_markers.fasta -out GCF_000330725.2_ASM33072v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:30,698] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:30,702] [INFO] Selected 28 target genomes.
[2024-01-24 13:28:30,702] [INFO] Target genome list was writen to GCF_000330725.2_ASM33072v2_genomic.fna/target_genomes.txt
[2024-01-24 13:28:30,728] [INFO] Task started: fastANI
[2024-01-24 13:28:30,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d36a12b-0414-4144-9898-425175385206/GCF_000330725.2_ASM33072v2_genomic.fna.gz --refList GCF_000330725.2_ASM33072v2_genomic.fna/target_genomes.txt --output GCF_000330725.2_ASM33072v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:56,478] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:56,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6d14439-e77f-4af8-887b-1ee8fbf3ce41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:56,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6d14439-e77f-4af8-887b-1ee8fbf3ce41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:56,491] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:56,491] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:56,492] [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
Mariniradius saccharolyticus	strain=AK6	GCA_000330725.2	1245591	1245591	type	True	100.0	1600	1601	95	conclusive
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	77.0356	261	1601	95	below_threshold
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	76.8966	164	1601	95	below_threshold
Cecembia rubra	strain=DSM 28057	GCA_003014575.1	1485585	1485585	type	True	76.7811	151	1601	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	76.6271	138	1601	95	below_threshold
Algoriphagus machipongonensis	strain=PR1	GCA_000166275.1	388413	388413	type	True	76.585	54	1601	95	below_threshold
Echinicola vietnamensis	strain=DSM 17526	GCA_000325705.1	390884	390884	type	True	76.4598	73	1601	95	below_threshold
Algoriphagus kandeliae	strain=XY-J91	GCA_004571135.1	2562278	2562278	type	True	76.349	79	1601	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	76.3146	108	1601	95	below_threshold
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	76.2429	116	1601	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	76.1501	64	1601	95	below_threshold
Algoriphagus oliviformis	strain=H41	GCA_017254915.1	2811231	2811231	type	True	76.1095	142	1601	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	76.0077	104	1601	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	75.9097	91	1601	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	75.7401	96	1601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:56,493] [INFO] DFAST Taxonomy check result was written to GCF_000330725.2_ASM33072v2_genomic.fna/tc_result.tsv
[2024-01-24 13:28:56,494] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:56,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:56,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6d14439-e77f-4af8-887b-1ee8fbf3ce41/dqc_reference/checkm_data
[2024-01-24 13:28:56,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:56,546] [INFO] Task started: CheckM
[2024-01-24 13:28:56,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000330725.2_ASM33072v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000330725.2_ASM33072v2_genomic.fna/checkm_input GCF_000330725.2_ASM33072v2_genomic.fna/checkm_result
[2024-01-24 13:30:18,215] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:18,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:18,233] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:18,233] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:18,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000330725.2_ASM33072v2_genomic.fna/markers.fasta)
[2024-01-24 13:30:18,234] [INFO] Task started: Blastn
[2024-01-24 13:30:18,234] [INFO] Running command: blastn -query GCF_000330725.2_ASM33072v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6d14439-e77f-4af8-887b-1ee8fbf3ce41/dqc_reference/reference_markers_gtdb.fasta -out GCF_000330725.2_ASM33072v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:18,984] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:18,987] [INFO] Selected 25 target genomes.
[2024-01-24 13:30:18,987] [INFO] Target genome list was writen to GCF_000330725.2_ASM33072v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:19,018] [INFO] Task started: fastANI
[2024-01-24 13:30:19,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d36a12b-0414-4144-9898-425175385206/GCF_000330725.2_ASM33072v2_genomic.fna.gz --refList GCF_000330725.2_ASM33072v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000330725.2_ASM33072v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:39,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:39,895] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:39,895] [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_000330725.2	s__Mariniradius saccharolyticus	100.0	1600	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mariniradius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003316845.1	s__Aquiflexum_A aquatile	77.0261	262	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	76.8966	164	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014575.1	s__Cecembia rubra	76.796	150	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	76.7616	115	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	76.7113	188	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	76.6127	139	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166275.1	s__Algoriphagus machipongonensis	76.585	54	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	76.4948	178	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000325705.1	s__Echinicola vietnamensis	76.4598	73	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583985.1	s__Algoriphagus lacus	76.3146	108	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254835.1	s__Algoriphagus aestuariicola	76.2589	115	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336015.1	s__Algoriphagus sp018336015	76.2339	115	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692705.1	s__Mongoliibacter sp007692705	76.1924	109	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	76.1501	64	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254915.1	s__Algoriphagus sp017254915	76.1219	141	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429445.1	s__Algoriphagus terrigena	76.0077	104	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259255.1	s__Algoriphagus litoralis	75.9196	92	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108085.1	s__Algoriphagus boritolerans	75.7401	96	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.80	99.80	0.99	0.99	2	-
GCA_014762705.1	s__Cyclobacterium sp014762705	75.5424	56	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:39,897] [INFO] GTDB search result was written to GCF_000330725.2_ASM33072v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:39,897] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:39,901] [INFO] DFAST_QC result json was written to GCF_000330725.2_ASM33072v2_genomic.fna/dqc_result.json
[2024-01-24 13:30:39,901] [INFO] DFAST_QC completed!
[2024-01-24 13:30:39,901] [INFO] Total running time: 0h2m41s