[2024-01-24 13:01:11,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:11,786] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:11,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg277b41fd-9b49-4f7c-9dbd-72ec40a5ee95/dqc_reference
[2024-01-24 13:01:13,069] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,070] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,070] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7e0e4f2-716e-47a9-89d5-7f7ff6eeef31/GCF_000425825.1_ASM42582v1_genomic.fna.gz | prodigal -d GCF_000425825.1_ASM42582v1_genomic.fna/cds.fna -a GCF_000425825.1_ASM42582v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:17,356] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:17,356] [INFO] Task started: HMMsearch
[2024-01-24 13:01:17,357] [INFO] Running command: hmmsearch --tblout GCF_000425825.1_ASM42582v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg277b41fd-9b49-4f7c-9dbd-72ec40a5ee95/dqc_reference/reference_markers.hmm GCF_000425825.1_ASM42582v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:17,624] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:17,625] [INFO] Found 6/6 markers.
[2024-01-24 13:01:17,648] [INFO] Query marker FASTA was written to GCF_000425825.1_ASM42582v1_genomic.fna/markers.fasta
[2024-01-24 13:01:17,648] [INFO] Task started: Blastn
[2024-01-24 13:01:17,648] [INFO] Running command: blastn -query GCF_000425825.1_ASM42582v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg277b41fd-9b49-4f7c-9dbd-72ec40a5ee95/dqc_reference/reference_markers.fasta -out GCF_000425825.1_ASM42582v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:18,251] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:18,255] [INFO] Selected 22 target genomes.
[2024-01-24 13:01:18,255] [INFO] Target genome list was writen to GCF_000425825.1_ASM42582v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:18,284] [INFO] Task started: fastANI
[2024-01-24 13:01:18,285] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7e0e4f2-716e-47a9-89d5-7f7ff6eeef31/GCF_000425825.1_ASM42582v1_genomic.fna.gz --refList GCF_000425825.1_ASM42582v1_genomic.fna/target_genomes.txt --output GCF_000425825.1_ASM42582v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:26,930] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:26,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg277b41fd-9b49-4f7c-9dbd-72ec40a5ee95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:26,931] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg277b41fd-9b49-4f7c-9dbd-72ec40a5ee95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:26,939] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:26,940] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:26,940] [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
Jeotgalicoccus marinus	strain=DSM 19772	GCA_000425825.1	516700	516700	type	True	100.0	690	691	95	conclusive
Jeotgalicoccus meleagridis	strain=CIP 111649	GCA_903994045.1	2759181	2759181	type	True	80.1617	360	691	95	below_threshold
Jeotgalicoccus psychrophilus	strain=DSM 19085	GCA_000425845.1	157228	157228	type	True	79.1541	245	691	95	below_threshold
Jeotgalicoccus halotolerans	strain=DSM 17274	GCA_003387165.1	157227	157227	type	True	79.1503	229	691	95	below_threshold
Jeotgalicoccus aerolatus	strain=CIP 111750	GCA_903994055.1	709510	709510	type	True	78.9604	240	691	95	below_threshold
Jeotgalicoccus aerolatus	strain=DSM 22420	GCA_017873755.1	709510	709510	type	True	78.9284	240	691	95	below_threshold
Jeotgalicoccus aerolatus	strain=CCM 7679	GCA_014635205.1	709510	709510	type	True	78.9165	244	691	95	below_threshold
Jeotgalicoccus saudimassiliensis	strain=13MG44_air	GCA_000756715.2	1461582	1461582	type	True	78.7375	210	691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:26,942] [INFO] DFAST Taxonomy check result was written to GCF_000425825.1_ASM42582v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:26,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:26,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:26,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg277b41fd-9b49-4f7c-9dbd-72ec40a5ee95/dqc_reference/checkm_data
[2024-01-24 13:01:26,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:26,967] [INFO] Task started: CheckM
[2024-01-24 13:01:26,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425825.1_ASM42582v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425825.1_ASM42582v1_genomic.fna/checkm_input GCF_000425825.1_ASM42582v1_genomic.fna/checkm_result
[2024-01-24 13:01:47,121] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:47,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:47,143] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:47,144] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:47,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425825.1_ASM42582v1_genomic.fna/markers.fasta)
[2024-01-24 13:01:47,144] [INFO] Task started: Blastn
[2024-01-24 13:01:47,145] [INFO] Running command: blastn -query GCF_000425825.1_ASM42582v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg277b41fd-9b49-4f7c-9dbd-72ec40a5ee95/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425825.1_ASM42582v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:47,927] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:47,930] [INFO] Selected 19 target genomes.
[2024-01-24 13:01:47,931] [INFO] Target genome list was writen to GCF_000425825.1_ASM42582v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:47,963] [INFO] Task started: fastANI
[2024-01-24 13:01:47,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7e0e4f2-716e-47a9-89d5-7f7ff6eeef31/GCF_000425825.1_ASM42582v1_genomic.fna.gz --refList GCF_000425825.1_ASM42582v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425825.1_ASM42582v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:01:55,375] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:55,383] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:01:55,384] [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_000425825.1	s__Jeotgalicoccus marinus	100.0	690	691	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	99.04	99.00	0.94	0.94	3	conclusive
GCF_903994045.1	s__Jeotgalicoccus meleagridis	80.1617	360	691	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	98.59	98.59	0.94	0.94	2	-
GCF_003387165.1	s__Jeotgalicoccus halotolerans	79.1692	230	691	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	96.2898	N/A	N/A	N/A	N/A	1	-
GCF_000425845.1	s__Jeotgalicoccus psychrophilus	79.1541	245	691	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	97.52	97.52	0.90	0.90	2	-
GCA_004570955.1	s__Jeotgalicoccus nanhaiensis	79.0216	236	691	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	96.2898	99.28	98.57	0.98	0.96	3	-
GCA_014635205.1	s__Jeotgalicoccus aerolatus	78.9181	243	691	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	99.67	99.03	0.98	0.93	4	-
GCF_000756715.1	s__Jeotgalicoccus saudimassiliensis	78.7375	210	691	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003513765.1	s__Jeotgalicoccus sp003513765	78.3446	217	691	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:01:55,388] [INFO] GTDB search result was written to GCF_000425825.1_ASM42582v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:01:55,389] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:01:55,393] [INFO] DFAST_QC result json was written to GCF_000425825.1_ASM42582v1_genomic.fna/dqc_result.json
[2024-01-24 13:01:55,393] [INFO] DFAST_QC completed!
[2024-01-24 13:01:55,393] [INFO] Total running time: 0h0m44s