[2024-01-25 18:03:20,457] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:20,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:20,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ec0cea0-848b-4e4f-96f2-b7b41552e255/dqc_reference
[2024-01-25 18:03:21,705] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:21,705] [INFO] Task started: Prodigal
[2024-01-25 18:03:21,706] [INFO] Running command: gunzip -c /var/lib/cwl/stgf885b056-ebf5-41d6-a79f-6b0545d9634e/GCF_000299295.2_ASM29929v2_genomic.fna.gz | prodigal -d GCF_000299295.2_ASM29929v2_genomic.fna/cds.fna -a GCF_000299295.2_ASM29929v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:27,220] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:27,220] [INFO] Task started: HMMsearch
[2024-01-25 18:03:27,221] [INFO] Running command: hmmsearch --tblout GCF_000299295.2_ASM29929v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ec0cea0-848b-4e4f-96f2-b7b41552e255/dqc_reference/reference_markers.hmm GCF_000299295.2_ASM29929v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:27,428] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:27,429] [INFO] Found 6/6 markers.
[2024-01-25 18:03:27,453] [INFO] Query marker FASTA was written to GCF_000299295.2_ASM29929v2_genomic.fna/markers.fasta
[2024-01-25 18:03:27,453] [INFO] Task started: Blastn
[2024-01-25 18:03:27,453] [INFO] Running command: blastn -query GCF_000299295.2_ASM29929v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ec0cea0-848b-4e4f-96f2-b7b41552e255/dqc_reference/reference_markers.fasta -out GCF_000299295.2_ASM29929v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:27,995] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:27,999] [INFO] Selected 12 target genomes.
[2024-01-25 18:03:28,000] [INFO] Target genome list was writen to GCF_000299295.2_ASM29929v2_genomic.fna/target_genomes.txt
[2024-01-25 18:03:28,013] [INFO] Task started: fastANI
[2024-01-25 18:03:28,013] [INFO] Running command: fastANI --query /var/lib/cwl/stgf885b056-ebf5-41d6-a79f-6b0545d9634e/GCF_000299295.2_ASM29929v2_genomic.fna.gz --refList GCF_000299295.2_ASM29929v2_genomic.fna/target_genomes.txt --output GCF_000299295.2_ASM29929v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:35,573] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:35,574] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ec0cea0-848b-4e4f-96f2-b7b41552e255/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:35,574] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ec0cea0-848b-4e4f-96f2-b7b41552e255/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:35,580] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:03:35,580] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:03:35,580] [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
Salimicrobium jeotgali	strain=MJ3	GCA_000299295.2	1230341	1230341	type	True	100.0	880	883	95	inconclusive
Salimicrobium jeotgali	strain=MJ3	GCA_001685435.3	1230341	1230341	type	True	99.9928	882	883	95	inconclusive
Salimicrobium humidisoli	strain=WN024	GCA_002295105.1	2029857	2029857	type	True	95.2578	751	883	95	inconclusive
Salimicrobium flavidum	strain=DSM 23127	GCA_900156645.1	570947	570947	type	True	78.8847	297	883	95	below_threshold
Salimicrobium halophilum	strain=DSM 4771	GCA_900100295.1	86666	86666	type	True	78.533	269	883	95	below_threshold
Halobacillus salinus	strain=HSL-3	GCA_004684905.1	192814	192814	type	True	77.3881	55	883	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:35,581] [INFO] DFAST Taxonomy check result was written to GCF_000299295.2_ASM29929v2_genomic.fna/tc_result.tsv
[2024-01-25 18:03:35,582] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:35,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:35,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ec0cea0-848b-4e4f-96f2-b7b41552e255/dqc_reference/checkm_data
[2024-01-25 18:03:35,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:35,612] [INFO] Task started: CheckM
[2024-01-25 18:03:35,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000299295.2_ASM29929v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000299295.2_ASM29929v2_genomic.fna/checkm_input GCF_000299295.2_ASM29929v2_genomic.fna/checkm_result
[2024-01-25 18:03:57,237] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:57,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:57,255] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:57,256] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:57,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000299295.2_ASM29929v2_genomic.fna/markers.fasta)
[2024-01-25 18:03:57,256] [INFO] Task started: Blastn
[2024-01-25 18:03:57,256] [INFO] Running command: blastn -query GCF_000299295.2_ASM29929v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ec0cea0-848b-4e4f-96f2-b7b41552e255/dqc_reference/reference_markers_gtdb.fasta -out GCF_000299295.2_ASM29929v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:57,999] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:58,002] [INFO] Selected 20 target genomes.
[2024-01-25 18:03:58,003] [INFO] Target genome list was writen to GCF_000299295.2_ASM29929v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:58,024] [INFO] Task started: fastANI
[2024-01-25 18:03:58,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgf885b056-ebf5-41d6-a79f-6b0545d9634e/GCF_000299295.2_ASM29929v2_genomic.fna.gz --refList GCF_000299295.2_ASM29929v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000299295.2_ASM29929v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:09,947] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:09,953] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 18:04:09,953] [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_900107115.1	s__Salimicrobium album	97.3842	768	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	97.70	97.32	0.90	0.88	5	inconclusive
GCF_002295105.1	s__Salimicrobium sp002295105	95.2578	751	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	98.33	98.33	0.92	0.92	2	inconclusive
GCF_000496835.1	s__Thalassobacillus devorans_B	78.9427	54	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156645.1	s__Salimicrobium flavidum	78.8847	297	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100295.1	s__Salimicrobium halophilum	78.5265	268	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991335.1	s__Halobacillus faecis	77.421	60	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684905.1	s__Halobacillus salinus	77.3881	55	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.08	98.08	0.93	0.93	2	-
GCF_900166625.1	s__Halobacillus_A massiliensis	77.1127	51	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:09,955] [INFO] GTDB search result was written to GCF_000299295.2_ASM29929v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:09,957] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:09,960] [INFO] DFAST_QC result json was written to GCF_000299295.2_ASM29929v2_genomic.fna/dqc_result.json
[2024-01-25 18:04:09,960] [INFO] DFAST_QC completed!
[2024-01-25 18:04:09,960] [INFO] Total running time: 0h0m50s