[2024-01-24 13:37:13,668] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:13,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:13,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg33b6e62e-53ec-41f5-a2ae-e2cafe676cd7/dqc_reference
[2024-01-24 13:37:14,921] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:14,922] [INFO] Task started: Prodigal
[2024-01-24 13:37:14,922] [INFO] Running command: gunzip -c /var/lib/cwl/stg45e71b2c-680a-4e6e-a087-b14c9fc1a0d7/GCF_008014775.1_ASM801477v1_genomic.fna.gz | prodigal -d GCF_008014775.1_ASM801477v1_genomic.fna/cds.fna -a GCF_008014775.1_ASM801477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:22,988] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:22,989] [INFO] Task started: HMMsearch
[2024-01-24 13:37:22,989] [INFO] Running command: hmmsearch --tblout GCF_008014775.1_ASM801477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33b6e62e-53ec-41f5-a2ae-e2cafe676cd7/dqc_reference/reference_markers.hmm GCF_008014775.1_ASM801477v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:23,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:23,255] [INFO] Found 6/6 markers.
[2024-01-24 13:37:23,288] [INFO] Query marker FASTA was written to GCF_008014775.1_ASM801477v1_genomic.fna/markers.fasta
[2024-01-24 13:37:23,288] [INFO] Task started: Blastn
[2024-01-24 13:37:23,288] [INFO] Running command: blastn -query GCF_008014775.1_ASM801477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33b6e62e-53ec-41f5-a2ae-e2cafe676cd7/dqc_reference/reference_markers.fasta -out GCF_008014775.1_ASM801477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:23,898] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:23,902] [INFO] Selected 21 target genomes.
[2024-01-24 13:37:23,902] [INFO] Target genome list was writen to GCF_008014775.1_ASM801477v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:23,926] [INFO] Task started: fastANI
[2024-01-24 13:37:23,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg45e71b2c-680a-4e6e-a087-b14c9fc1a0d7/GCF_008014775.1_ASM801477v1_genomic.fna.gz --refList GCF_008014775.1_ASM801477v1_genomic.fna/target_genomes.txt --output GCF_008014775.1_ASM801477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:39,676] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:39,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33b6e62e-53ec-41f5-a2ae-e2cafe676cd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:39,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33b6e62e-53ec-41f5-a2ae-e2cafe676cd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:39,688] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:39,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:39,688] [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
Alkalicoccus halolimnae	strain=BZ-SZ-XJ29	GCA_008014775.1	1667239	1667239	type	True	100.0	1195	1196	95	conclusive
Alkalicoccus saliphilus	strain=6AG	GCA_003044065.1	200989	200989	type	True	78.3222	300	1196	95	below_threshold
Alkalicoccus daliensis	strain=CGMCC 1.10369	GCA_900103955.1	745820	745820	type	True	77.5354	207	1196	95	below_threshold
Alkalicoccus urumqiensis	strain=BZ-SZ-XJ18	GCA_002993335.1	1548213	1548213	type	True	77.1305	142	1196	95	below_threshold
Paenalkalicoccus suaedae	strain=M4U3P1	GCA_006965545.2	2592382	2592382	type	True	76.8471	66	1196	95	below_threshold
Alteribacter salitolerans	strain=APA H-16(1)	GCA_016901055.1	2912333	2912333	type	True	76.7752	58	1196	95	below_threshold
Salipaludibacillus aurantiacus	strain=S9	GCA_900111295.1	1601833	1601833	type	True	76.7673	80	1196	95	below_threshold
Alkalicoccus chagannorensis	strain=DSM 18086	GCA_000429725.1	427072	427072	type	True	76.7186	123	1196	95	below_threshold
Alteribacter keqinensis	strain=KQ-3	GCA_003710255.1	2483800	2483800	type	True	76.5982	59	1196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:39,690] [INFO] DFAST Taxonomy check result was written to GCF_008014775.1_ASM801477v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:39,690] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:39,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:39,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33b6e62e-53ec-41f5-a2ae-e2cafe676cd7/dqc_reference/checkm_data
[2024-01-24 13:37:39,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:39,736] [INFO] Task started: CheckM
[2024-01-24 13:37:39,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008014775.1_ASM801477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008014775.1_ASM801477v1_genomic.fna/checkm_input GCF_008014775.1_ASM801477v1_genomic.fna/checkm_result
[2024-01-24 13:38:09,809] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:09,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:09,830] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:09,830] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:09,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008014775.1_ASM801477v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:09,831] [INFO] Task started: Blastn
[2024-01-24 13:38:09,831] [INFO] Running command: blastn -query GCF_008014775.1_ASM801477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33b6e62e-53ec-41f5-a2ae-e2cafe676cd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_008014775.1_ASM801477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:10,628] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:10,632] [INFO] Selected 18 target genomes.
[2024-01-24 13:38:10,632] [INFO] Target genome list was writen to GCF_008014775.1_ASM801477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:10,680] [INFO] Task started: fastANI
[2024-01-24 13:38:10,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg45e71b2c-680a-4e6e-a087-b14c9fc1a0d7/GCF_008014775.1_ASM801477v1_genomic.fna.gz --refList GCF_008014775.1_ASM801477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008014775.1_ASM801477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:23,294] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:23,311] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:23,311] [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_008014775.1	s__Alkalicoccus halolimnae	100.0	1195	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003044065.1	s__Alkalicoccus saliphilus	78.3751	295	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692495.1	s__Alkalicoccus sp007692495	78.0962	238	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003560495.1	s__Alkalicoccus sp003560495	78.0816	227	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	99.31	99.31	0.92	0.92	2	-
GCF_900103955.1	s__Alkalicoccus daliensis	77.5222	208	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993335.1	s__Alkalicoccus urumqiensis	77.1305	142	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034335.1	s__Alkalicoccus luteus	77.1193	144	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710255.1	s__Alteribacter sp003710255	76.6538	60	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	98.04	98.04	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:23,317] [INFO] GTDB search result was written to GCF_008014775.1_ASM801477v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:23,319] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:23,323] [INFO] DFAST_QC result json was written to GCF_008014775.1_ASM801477v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:23,324] [INFO] DFAST_QC completed!
[2024-01-24 13:38:23,324] [INFO] Total running time: 0h1m10s