[2024-01-24 12:21:57,766] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgc540ad6f-8f55-4dea-9a69-2e7488b0dd4f/dqc_reference
[2024-01-24 12:21:59,052] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:59,053] [INFO] Task started: Prodigal
[2024-01-24 12:21:59,053] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a29d294-4d0b-4719-8f14-746a166e6a11/GCF_003308995.1_ASM330899v1_genomic.fna.gz | prodigal -d GCF_003308995.1_ASM330899v1_genomic.fna/cds.fna -a GCF_003308995.1_ASM330899v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:50,392] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:50,393] [INFO] Task started: HMMsearch
[2024-01-24 12:22:50,393] [INFO] Running command: hmmsearch --tblout GCF_003308995.1_ASM330899v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc540ad6f-8f55-4dea-9a69-2e7488b0dd4f/dqc_reference/reference_markers.hmm GCF_003308995.1_ASM330899v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:50,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:50,799] [INFO] Found 6/6 markers.
[2024-01-24 12:22:50,865] [INFO] Query marker FASTA was written to GCF_003308995.1_ASM330899v1_genomic.fna/markers.fasta
[2024-01-24 12:22:50,865] [INFO] Task started: Blastn
[2024-01-24 12:22:50,866] [INFO] Running command: blastn -query GCF_003308995.1_ASM330899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc540ad6f-8f55-4dea-9a69-2e7488b0dd4f/dqc_reference/reference_markers.fasta -out GCF_003308995.1_ASM330899v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:51,487] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:51,491] [INFO] Selected 11 target genomes.
[2024-01-24 12:22:51,491] [INFO] Target genome list was writen to GCF_003308995.1_ASM330899v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:51,493] [INFO] Task started: fastANI
[2024-01-24 12:22:51,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a29d294-4d0b-4719-8f14-746a166e6a11/GCF_003308995.1_ASM330899v1_genomic.fna.gz --refList GCF_003308995.1_ASM330899v1_genomic.fna/target_genomes.txt --output GCF_003308995.1_ASM330899v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:07,902] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:07,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc540ad6f-8f55-4dea-9a69-2e7488b0dd4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:07,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc540ad6f-8f55-4dea-9a69-2e7488b0dd4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:07,912] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:07,912] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:07,912] [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
Chitinophaga flava	strain=GDMCC 1.1325	GCA_003308995.1	2259036	2259036	type	True	100.0	2781	2781	95	conclusive
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	82.0141	1557	2781	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	81.8187	1451	2781	95	below_threshold
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	81.7816	1563	2781	95	below_threshold
Chitinophaga eiseniae	strain=DSM 22224	GCA_900167135.1	634771	634771	type	True	81.7057	1426	2781	95	below_threshold
Chitinophaga oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	81.6994	1401	2781	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	79.3087	801	2781	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	75.626	75	2781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:07,914] [INFO] DFAST Taxonomy check result was written to GCF_003308995.1_ASM330899v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:07,914] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:07,914] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:07,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc540ad6f-8f55-4dea-9a69-2e7488b0dd4f/dqc_reference/checkm_data
[2024-01-24 12:23:07,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:07,992] [INFO] Task started: CheckM
[2024-01-24 12:23:07,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003308995.1_ASM330899v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003308995.1_ASM330899v1_genomic.fna/checkm_input GCF_003308995.1_ASM330899v1_genomic.fna/checkm_result
[2024-01-24 12:25:22,444] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:22,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:22,466] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:22,467] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:22,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003308995.1_ASM330899v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:22,467] [INFO] Task started: Blastn
[2024-01-24 12:25:22,467] [INFO] Running command: blastn -query GCF_003308995.1_ASM330899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc540ad6f-8f55-4dea-9a69-2e7488b0dd4f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003308995.1_ASM330899v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:23,218] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:23,222] [INFO] Selected 8 target genomes.
[2024-01-24 12:25:23,222] [INFO] Target genome list was writen to GCF_003308995.1_ASM330899v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:23,224] [INFO] Task started: fastANI
[2024-01-24 12:25:23,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a29d294-4d0b-4719-8f14-746a166e6a11/GCF_003308995.1_ASM330899v1_genomic.fna.gz --refList GCF_003308995.1_ASM330899v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003308995.1_ASM330899v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:37,365] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:37,373] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:37,373] [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_003308995.1	s__Chitinophaga flava	100.0	2781	2781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018255755.1	s__Chitinophaga sp018255755	92.9385	2357	2781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927205.1	s__Chitinophaga fulva	82.0172	1556	2781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014529935.1	s__Chitinophaga qingshengii	81.8313	1448	2781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014529945.1	s__Chitinophaga varians	81.7809	1564	2781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641275.1	s__Chitinophaga varians_A	81.7261	1527	2781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167135.1	s__Chitinophaga eiseniae	81.7245	1421	2781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012516355.1	s__Chitinophaga sp012516355	81.6756	1420	2781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.48	99.48	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:37,375] [INFO] GTDB search result was written to GCF_003308995.1_ASM330899v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:37,376] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:37,378] [INFO] DFAST_QC result json was written to GCF_003308995.1_ASM330899v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:37,379] [INFO] DFAST_QC completed!
[2024-01-24 12:25:37,379] [INFO] Total running time: 0h3m40s