[2024-01-24 13:36:32,039] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,043] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,043] [INFO] DQC Reference Directory: /var/lib/cwl/stg67695d6d-c0b4-44ca-95b8-53b22a3d7b7d/dqc_reference
[2024-01-24 13:36:33,365] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,366] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg49d186d1-5792-4edb-8d28-f0545c5a4994/GCF_000428725.1_ASM42872v1_genomic.fna.gz | prodigal -d GCF_000428725.1_ASM42872v1_genomic.fna/cds.fna -a GCF_000428725.1_ASM42872v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:43,586] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:43,586] [INFO] Task started: HMMsearch
[2024-01-24 13:36:43,586] [INFO] Running command: hmmsearch --tblout GCF_000428725.1_ASM42872v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67695d6d-c0b4-44ca-95b8-53b22a3d7b7d/dqc_reference/reference_markers.hmm GCF_000428725.1_ASM42872v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:43,925] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:43,927] [INFO] Found 6/6 markers.
[2024-01-24 13:36:43,970] [INFO] Query marker FASTA was written to GCF_000428725.1_ASM42872v1_genomic.fna/markers.fasta
[2024-01-24 13:36:43,971] [INFO] Task started: Blastn
[2024-01-24 13:36:43,971] [INFO] Running command: blastn -query GCF_000428725.1_ASM42872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67695d6d-c0b4-44ca-95b8-53b22a3d7b7d/dqc_reference/reference_markers.fasta -out GCF_000428725.1_ASM42872v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:44,707] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:44,712] [INFO] Selected 16 target genomes.
[2024-01-24 13:36:44,712] [INFO] Target genome list was writen to GCF_000428725.1_ASM42872v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:44,723] [INFO] Task started: fastANI
[2024-01-24 13:36:44,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d186d1-5792-4edb-8d28-f0545c5a4994/GCF_000428725.1_ASM42872v1_genomic.fna.gz --refList GCF_000428725.1_ASM42872v1_genomic.fna/target_genomes.txt --output GCF_000428725.1_ASM42872v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:58,134] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:58,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67695d6d-c0b4-44ca-95b8-53b22a3d7b7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:58,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67695d6d-c0b4-44ca-95b8-53b22a3d7b7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:58,149] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:58,149] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:58,149] [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
Psychromonas aquimarina	strain=ATCC BAA-1526	GCA_000428725.1	444919	444919	type	True	100.0	1775	1778	95	conclusive
Psychromonas ossibalaenae	strain=JAMM 0738	GCA_000381745.1	444922	444922	type	True	88.5028	1329	1778	95	below_threshold
Psychromonas antarctica	strain=DSM 10704	GCA_022267535.1	67573	67573	type	True	78.5098	340	1778	95	below_threshold
Psychromonas ingrahamii	strain=37	GCA_000015285.1	357794	357794	type	True	78.1611	313	1778	95	below_threshold
Psychromonas arctica	strain=DSM 14288	GCA_000482725.1	168275	168275	type	True	78.1375	238	1778	95	below_threshold
Psychromonas hadalis	strain=ATCC BAA-638	GCA_000420245.1	211669	211669	type	True	78.0766	280	1778	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	76.7082	79	1778	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:58,151] [INFO] DFAST Taxonomy check result was written to GCF_000428725.1_ASM42872v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:58,151] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:58,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:58,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67695d6d-c0b4-44ca-95b8-53b22a3d7b7d/dqc_reference/checkm_data
[2024-01-24 13:36:58,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:58,208] [INFO] Task started: CheckM
[2024-01-24 13:36:58,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428725.1_ASM42872v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428725.1_ASM42872v1_genomic.fna/checkm_input GCF_000428725.1_ASM42872v1_genomic.fna/checkm_result
[2024-01-24 13:37:35,238] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:35,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,258] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:35,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:35,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428725.1_ASM42872v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:35,259] [INFO] Task started: Blastn
[2024-01-24 13:37:35,260] [INFO] Running command: blastn -query GCF_000428725.1_ASM42872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67695d6d-c0b4-44ca-95b8-53b22a3d7b7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428725.1_ASM42872v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:36,466] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:36,470] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:36,470] [INFO] Target genome list was writen to GCF_000428725.1_ASM42872v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:36,484] [INFO] Task started: fastANI
[2024-01-24 13:37:36,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d186d1-5792-4edb-8d28-f0545c5a4994/GCF_000428725.1_ASM42872v1_genomic.fna.gz --refList GCF_000428725.1_ASM42872v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428725.1_ASM42872v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:45,958] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:45,967] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:45,968] [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_000428725.1	s__Psychromonas aquimarina	100.0	1775	1778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000381745.1	s__Psychromonas ossibalaenae	88.4938	1331	1778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013619145.1	s__Psychromonas sp013619145	80.4209	587	1778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004376845.1	s__Psychromonas sp004376845	78.5915	203	1778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835465.1	s__Psychromonas sp002835465	78.5324	254	1778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835995.1	s__Psychromonas sp002835995	78.4301	304	1778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836415.1	s__Psychromonas sp002836415	78.2527	318	1778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482725.1	s__Psychromonas arctica	78.1931	237	1778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	98.18	98.18	0.89	0.89	2	-
GCF_000015285.1	s__Psychromonas ingrahamii	78.1439	308	1778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:45,970] [INFO] GTDB search result was written to GCF_000428725.1_ASM42872v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:45,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:45,974] [INFO] DFAST_QC result json was written to GCF_000428725.1_ASM42872v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:45,974] [INFO] DFAST_QC completed!
[2024-01-24 13:37:45,974] [INFO] Total running time: 0h1m14s