[2024-01-24 14:30:34,602] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:34,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:34,609] [INFO] DQC Reference Directory: /var/lib/cwl/stgb677703b-c7df-484d-a403-380103dc1c26/dqc_reference
[2024-01-24 14:30:35,972] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:35,973] [INFO] Task started: Prodigal
[2024-01-24 14:30:35,974] [INFO] Running command: gunzip -c /var/lib/cwl/stgb69f4c74-143d-4b6d-a62b-909fd9617fe2/GCF_014206875.1_ASM1420687v1_genomic.fna.gz | prodigal -d GCF_014206875.1_ASM1420687v1_genomic.fna/cds.fna -a GCF_014206875.1_ASM1420687v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:01,107] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:01,108] [INFO] Task started: HMMsearch
[2024-01-24 14:31:01,108] [INFO] Running command: hmmsearch --tblout GCF_014206875.1_ASM1420687v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb677703b-c7df-484d-a403-380103dc1c26/dqc_reference/reference_markers.hmm GCF_014206875.1_ASM1420687v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:01,483] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:01,485] [INFO] Found 6/6 markers.
[2024-01-24 14:31:01,549] [INFO] Query marker FASTA was written to GCF_014206875.1_ASM1420687v1_genomic.fna/markers.fasta
[2024-01-24 14:31:01,550] [INFO] Task started: Blastn
[2024-01-24 14:31:01,550] [INFO] Running command: blastn -query GCF_014206875.1_ASM1420687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb677703b-c7df-484d-a403-380103dc1c26/dqc_reference/reference_markers.fasta -out GCF_014206875.1_ASM1420687v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:02,268] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:02,272] [INFO] Selected 10 target genomes.
[2024-01-24 14:31:02,273] [INFO] Target genome list was writen to GCF_014206875.1_ASM1420687v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:02,279] [INFO] Task started: fastANI
[2024-01-24 14:31:02,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgb69f4c74-143d-4b6d-a62b-909fd9617fe2/GCF_014206875.1_ASM1420687v1_genomic.fna.gz --refList GCF_014206875.1_ASM1420687v1_genomic.fna/target_genomes.txt --output GCF_014206875.1_ASM1420687v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:12,500] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:12,501] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb677703b-c7df-484d-a403-380103dc1c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:12,501] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb677703b-c7df-484d-a403-380103dc1c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:12,510] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:12,511] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:12,511] [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
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	100.0	1805	1805	95	conclusive
Algoriphagus machipongonensis	strain=PR1	GCA_000166275.1	388413	388413	type	True	80.8001	777	1805	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	80.0736	867	1805	95	below_threshold
Algoriphagus halophilus	strain=DSM 15292	GCA_900129785.1	226505	226505	type	True	79.7564	731	1805	95	below_threshold
Algoriphagus lutimaris	strain=KCTC 22630	GCA_017051705.1	613197	613197	type	True	79.6998	700	1805	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	77.9415	380	1805	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.8476	378	1805	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	77.8074	411	1805	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	76.6625	115	1805	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:12,512] [INFO] DFAST Taxonomy check result was written to GCF_014206875.1_ASM1420687v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:12,513] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:12,513] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:12,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb677703b-c7df-484d-a403-380103dc1c26/dqc_reference/checkm_data
[2024-01-24 14:31:12,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:12,569] [INFO] Task started: CheckM
[2024-01-24 14:31:12,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014206875.1_ASM1420687v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014206875.1_ASM1420687v1_genomic.fna/checkm_input GCF_014206875.1_ASM1420687v1_genomic.fna/checkm_result
[2024-01-24 14:32:23,655] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:23,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:23,678] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:23,679] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:23,679] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014206875.1_ASM1420687v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:23,679] [INFO] Task started: Blastn
[2024-01-24 14:32:23,680] [INFO] Running command: blastn -query GCF_014206875.1_ASM1420687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb677703b-c7df-484d-a403-380103dc1c26/dqc_reference/reference_markers_gtdb.fasta -out GCF_014206875.1_ASM1420687v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:24,465] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:24,469] [INFO] Selected 12 target genomes.
[2024-01-24 14:32:24,469] [INFO] Target genome list was writen to GCF_014206875.1_ASM1420687v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:24,477] [INFO] Task started: fastANI
[2024-01-24 14:32:24,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgb69f4c74-143d-4b6d-a62b-909fd9617fe2/GCF_014206875.1_ASM1420687v1_genomic.fna.gz --refList GCF_014206875.1_ASM1420687v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014206875.1_ASM1420687v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:35,814] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:35,827] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:35,827] [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_014206875.1	s__Algoriphagus iocasae	100.0	1805	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000166275.1	s__Algoriphagus machipongonensis	80.8084	776	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	80.0862	865	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129785.1	s__Algoriphagus halophilus	79.7733	729	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051705.1	s__Algoriphagus lutimaris	79.6922	701	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997215.1	s__Algoriphagus aquimarinus_A	79.2316	425	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	78.0948	369	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	77.9204	380	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	77.8465	378	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	77.8082	411	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885605.1	s__Algoriphagus sp009885605	77.5993	192	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115305.1	s__Algoriphagus ornithinivorans	77.5779	284	1805	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	95.91	95.63	0.88	0.85	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:35,829] [INFO] GTDB search result was written to GCF_014206875.1_ASM1420687v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:35,830] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:35,836] [INFO] DFAST_QC result json was written to GCF_014206875.1_ASM1420687v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:35,836] [INFO] DFAST_QC completed!
[2024-01-24 14:32:35,836] [INFO] Total running time: 0h2m1s