[2024-01-24 15:27:02,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:02,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:02,549] [INFO] DQC Reference Directory: /var/lib/cwl/stgd74b83c1-a66f-4213-aa99-54960ada5efe/dqc_reference
[2024-01-24 15:27:03,742] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:03,743] [INFO] Task started: Prodigal
[2024-01-24 15:27:03,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg74b95d1c-71a0-425a-892b-28b900a9d614/GCF_004402695.1_ASM440269v1_genomic.fna.gz | prodigal -d GCF_004402695.1_ASM440269v1_genomic.fna/cds.fna -a GCF_004402695.1_ASM440269v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:14,697] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:14,698] [INFO] Task started: HMMsearch
[2024-01-24 15:27:14,698] [INFO] Running command: hmmsearch --tblout GCF_004402695.1_ASM440269v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd74b83c1-a66f-4213-aa99-54960ada5efe/dqc_reference/reference_markers.hmm GCF_004402695.1_ASM440269v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:14,954] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:14,955] [INFO] Found 6/6 markers.
[2024-01-24 15:27:14,986] [INFO] Query marker FASTA was written to GCF_004402695.1_ASM440269v1_genomic.fna/markers.fasta
[2024-01-24 15:27:14,987] [INFO] Task started: Blastn
[2024-01-24 15:27:14,987] [INFO] Running command: blastn -query GCF_004402695.1_ASM440269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd74b83c1-a66f-4213-aa99-54960ada5efe/dqc_reference/reference_markers.fasta -out GCF_004402695.1_ASM440269v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:16,140] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:16,144] [INFO] Selected 13 target genomes.
[2024-01-24 15:27:16,144] [INFO] Target genome list was writen to GCF_004402695.1_ASM440269v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:16,150] [INFO] Task started: fastANI
[2024-01-24 15:27:16,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b95d1c-71a0-425a-892b-28b900a9d614/GCF_004402695.1_ASM440269v1_genomic.fna.gz --refList GCF_004402695.1_ASM440269v1_genomic.fna/target_genomes.txt --output GCF_004402695.1_ASM440269v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:26,408] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:26,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd74b83c1-a66f-4213-aa99-54960ada5efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:26,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd74b83c1-a66f-4213-aa99-54960ada5efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:26,419] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:26,419] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:26,420] [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
Cryobacterium zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	90.7283	964	1193	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	86.1157	894	1193	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	85.8311	917	1193	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	81.3523	535	1193	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	81.3185	540	1193	95	below_threshold
Cryobacterium breve	strain=TMT4-23	GCA_004402375.1	1259258	1259258	type	True	80.9676	572	1193	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	80.6996	560	1193	95	below_threshold
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	79.9727	480	1193	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	79.9572	502	1193	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	79.8924	483	1193	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.765	361	1193	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.7112	411	1193	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.6482	381	1193	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:26,421] [INFO] DFAST Taxonomy check result was written to GCF_004402695.1_ASM440269v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:26,422] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:26,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:26,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd74b83c1-a66f-4213-aa99-54960ada5efe/dqc_reference/checkm_data
[2024-01-24 15:27:26,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:26,461] [INFO] Task started: CheckM
[2024-01-24 15:27:26,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004402695.1_ASM440269v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004402695.1_ASM440269v1_genomic.fna/checkm_input GCF_004402695.1_ASM440269v1_genomic.fna/checkm_result
[2024-01-24 15:28:01,764] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:01,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:01,787] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:01,787] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:01,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004402695.1_ASM440269v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:01,788] [INFO] Task started: Blastn
[2024-01-24 15:28:01,788] [INFO] Running command: blastn -query GCF_004402695.1_ASM440269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd74b83c1-a66f-4213-aa99-54960ada5efe/dqc_reference/reference_markers_gtdb.fasta -out GCF_004402695.1_ASM440269v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:03,666] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:03,670] [INFO] Selected 7 target genomes.
[2024-01-24 15:28:03,670] [INFO] Target genome list was writen to GCF_004402695.1_ASM440269v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:03,677] [INFO] Task started: fastANI
[2024-01-24 15:28:03,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b95d1c-71a0-425a-892b-28b900a9d614/GCF_004402695.1_ASM440269v1_genomic.fna.gz --refList GCF_004402695.1_ASM440269v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004402695.1_ASM440269v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:10,786] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:10,800] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:10,800] [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_004402695.1	s__Cryobacterium sp004402695	100.0	1188	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002929555.1	s__Cryobacterium sp002929555	91.7284	972	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909375.1	s__Cryobacterium zongtaii	90.7283	964	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.98	96.32	0.90	0.86	11	-
GCF_004403945.1	s__Cryobacterium sp004403945	88.2105	944	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004210215.1	s__Cryobacterium sp004210215	87.9223	878	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679725.1	s__Cryobacterium arcticum_A	86.1844	931	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185895.1	s__Cryobacterium arcticum	85.8389	916	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:10,802] [INFO] GTDB search result was written to GCF_004402695.1_ASM440269v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:10,802] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:10,838] [INFO] DFAST_QC result json was written to GCF_004402695.1_ASM440269v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:10,838] [INFO] DFAST_QC completed!
[2024-01-24 15:28:10,838] [INFO] Total running time: 0h1m8s