[2024-01-24 11:26:28,085] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,087] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,087] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2fee1ba-dd95-44f6-932d-07164b26ac8c/dqc_reference
[2024-01-24 11:26:29,412] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,413] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c767c14-6892-4e85-852e-70c4c11324e6/GCF_002807035.1_ASM280703v1_genomic.fna.gz | prodigal -d GCF_002807035.1_ASM280703v1_genomic.fna/cds.fna -a GCF_002807035.1_ASM280703v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:50,553] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:50,553] [INFO] Task started: HMMsearch
[2024-01-24 11:26:50,554] [INFO] Running command: hmmsearch --tblout GCF_002807035.1_ASM280703v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2fee1ba-dd95-44f6-932d-07164b26ac8c/dqc_reference/reference_markers.hmm GCF_002807035.1_ASM280703v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:50,893] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:50,895] [INFO] Found 6/6 markers.
[2024-01-24 11:26:50,959] [INFO] Query marker FASTA was written to GCF_002807035.1_ASM280703v1_genomic.fna/markers.fasta
[2024-01-24 11:26:50,960] [INFO] Task started: Blastn
[2024-01-24 11:26:50,960] [INFO] Running command: blastn -query GCF_002807035.1_ASM280703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2fee1ba-dd95-44f6-932d-07164b26ac8c/dqc_reference/reference_markers.fasta -out GCF_002807035.1_ASM280703v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:51,579] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:51,582] [INFO] Selected 17 target genomes.
[2024-01-24 11:26:51,583] [INFO] Target genome list was writen to GCF_002807035.1_ASM280703v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:51,589] [INFO] Task started: fastANI
[2024-01-24 11:26:51,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c767c14-6892-4e85-852e-70c4c11324e6/GCF_002807035.1_ASM280703v1_genomic.fna.gz --refList GCF_002807035.1_ASM280703v1_genomic.fna/target_genomes.txt --output GCF_002807035.1_ASM280703v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:05,965] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:05,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2fee1ba-dd95-44f6-932d-07164b26ac8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:05,966] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2fee1ba-dd95-44f6-932d-07164b26ac8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:05,980] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:05,980] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:27:05,980] [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 formosus	strain=XAY3209	GCA_002807035.1	2007308	2007308	type	True	100.0	1492	1493	95	inconclusive
Algoriphagus aquimaris	strain=F21	GCA_004358035.1	2547398	2547398	type	True	97.542	1335	1493	95	inconclusive
Algoriphagus marincola	strain=DSM 16067	GCA_000429405.1	264027	264027	type	True	93.2422	1267	1493	95	below_threshold
Algoriphagus faecimaris	strain=JCM 16561	GCA_002150585.1	686796	686796	type	True	78.5721	381	1493	95	below_threshold
Algoriphagus kandeliae	strain=XY-J91	GCA_004571135.1	2562278	2562278	type	True	78.4538	458	1493	95	below_threshold
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	77.9814	317	1493	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	77.8232	334	1493	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	77.3585	291	1493	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.3547	296	1493	95	below_threshold
Algoriphagus locisalis	strain=DSM 23445	GCA_900116615.1	305507	305507	type	True	76.9455	154	1493	95	below_threshold
Algoriphagus mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	76.8889	222	1493	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_003387655.1	238540	238540	type	True	76.6034	160	1493	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	76.5363	73	1493	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	76.4621	158	1493	95	below_threshold
Cyclobacterium roseum	strain=SYSU L10180	GCA_010119225.1	2666137	2666137	type	True	76.3353	53	1493	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	76.1759	65	1493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:05,991] [INFO] DFAST Taxonomy check result was written to GCF_002807035.1_ASM280703v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:05,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:05,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:05,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2fee1ba-dd95-44f6-932d-07164b26ac8c/dqc_reference/checkm_data
[2024-01-24 11:27:05,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:06,040] [INFO] Task started: CheckM
[2024-01-24 11:27:06,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002807035.1_ASM280703v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002807035.1_ASM280703v1_genomic.fna/checkm_input GCF_002807035.1_ASM280703v1_genomic.fna/checkm_result
[2024-01-24 11:28:07,608] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:07,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:07,631] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:07,631] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:07,632] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002807035.1_ASM280703v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:07,632] [INFO] Task started: Blastn
[2024-01-24 11:28:07,632] [INFO] Running command: blastn -query GCF_002807035.1_ASM280703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2fee1ba-dd95-44f6-932d-07164b26ac8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002807035.1_ASM280703v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:08,409] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:08,412] [INFO] Selected 11 target genomes.
[2024-01-24 11:28:08,412] [INFO] Target genome list was writen to GCF_002807035.1_ASM280703v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:08,420] [INFO] Task started: fastANI
[2024-01-24 11:28:08,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c767c14-6892-4e85-852e-70c4c11324e6/GCF_002807035.1_ASM280703v1_genomic.fna.gz --refList GCF_002807035.1_ASM280703v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002807035.1_ASM280703v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:18,451] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:18,465] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:18,465] [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_002807035.1	s__Algoriphagus formosus	100.0	1492	1493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.55	97.55	0.93	0.93	2	conclusive
GCF_000526355.1	s__Algoriphagus marincola_A	93.7236	1167	1493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000429405.1	s__Algoriphagus marincola	93.2571	1266	1493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.35	97.35	0.90	0.90	2	-
GCA_013373335.1	s__Algoriphagus sp013373335	79.1311	371	1493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101705.1	s__Algoriphagus faecimaris	78.5354	379	1493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	0.98	0.98	2	-
GCA_013373065.1	s__Algoriphagus sp013373065	78.5147	434	1493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571135.1	s__Algoriphagus kandeliae	78.4538	458	1493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113375.1	s__Algoriphagus hitonicola	77.8299	334	1493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429425.1	s__Algoriphagus mannitolivorans	76.8877	221	1493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838715.1	s__Algoriphagus sp014838715	76.8308	156	1493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150685.1	s__Algoriphagus antarcticus	76.4665	159	1493	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:18,467] [INFO] GTDB search result was written to GCF_002807035.1_ASM280703v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:18,467] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:18,471] [INFO] DFAST_QC result json was written to GCF_002807035.1_ASM280703v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:18,471] [INFO] DFAST_QC completed!
[2024-01-24 11:28:18,471] [INFO] Total running time: 0h1m50s