[2023-06-30 04:51:45,066] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:51:45,069] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:51:45,069] [INFO] DQC Reference Directory: /var/lib/cwl/stg98681710-e107-4d56-86b2-91085ab3bbda/dqc_reference
[2023-06-30 04:51:46,376] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:51:46,377] [INFO] Task started: Prodigal
[2023-06-30 04:51:46,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d2827d3-27f6-475d-8335-32922e7b051c/GCA_024103175.1_ASM2410317v1_genomic.fna.gz | prodigal -d GCA_024103175.1_ASM2410317v1_genomic.fna/cds.fna -a GCA_024103175.1_ASM2410317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:52:25,551] [INFO] Task succeeded: Prodigal
[2023-06-30 04:52:25,551] [INFO] Task started: HMMsearch
[2023-06-30 04:52:25,551] [INFO] Running command: hmmsearch --tblout GCA_024103175.1_ASM2410317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98681710-e107-4d56-86b2-91085ab3bbda/dqc_reference/reference_markers.hmm GCA_024103175.1_ASM2410317v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:52:25,890] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:52:25,891] [INFO] Found 6/6 markers.
[2023-06-30 04:52:25,953] [INFO] Query marker FASTA was written to GCA_024103175.1_ASM2410317v1_genomic.fna/markers.fasta
[2023-06-30 04:52:25,954] [INFO] Task started: Blastn
[2023-06-30 04:52:25,954] [INFO] Running command: blastn -query GCA_024103175.1_ASM2410317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98681710-e107-4d56-86b2-91085ab3bbda/dqc_reference/reference_markers.fasta -out GCA_024103175.1_ASM2410317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:52:26,579] [INFO] Task succeeded: Blastn
[2023-06-30 04:52:26,585] [INFO] Selected 24 target genomes.
[2023-06-30 04:52:26,585] [INFO] Target genome list was writen to GCA_024103175.1_ASM2410317v1_genomic.fna/target_genomes.txt
[2023-06-30 04:52:26,587] [INFO] Task started: fastANI
[2023-06-30 04:52:26,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d2827d3-27f6-475d-8335-32922e7b051c/GCA_024103175.1_ASM2410317v1_genomic.fna.gz --refList GCA_024103175.1_ASM2410317v1_genomic.fna/target_genomes.txt --output GCA_024103175.1_ASM2410317v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:52:44,495] [INFO] Task succeeded: fastANI
[2023-06-30 04:52:44,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98681710-e107-4d56-86b2-91085ab3bbda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:52:44,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98681710-e107-4d56-86b2-91085ab3bbda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:52:44,510] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:52:44,510] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 04:52:44,510] [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
Phaeodactylibacter xiamenensis	strain=KD52	GCA_000759025.1	1524460	1524460	type	True	76.0277	155	2221	95	below_threshold
Phaeodactylibacter luteus	strain=KCTC 42180	GCA_007993045.1	1564516	1564516	type	True	75.8555	123	2221	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	75.8456	132	2221	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	75.8436	130	2221	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	75.7573	86	2221	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	75.5502	57	2221	95	below_threshold
Hymenobacter gummosus	strain=KCTC 52166	GCA_003970915.1	1776032	1776032	type	True	75.4687	88	2221	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	75.3147	89	2221	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	75.0409	76	2221	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 04:52:44,512] [INFO] DFAST Taxonomy check result was written to GCA_024103175.1_ASM2410317v1_genomic.fna/tc_result.tsv
[2023-06-30 04:52:44,513] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:52:44,513] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:52:44,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98681710-e107-4d56-86b2-91085ab3bbda/dqc_reference/checkm_data
[2023-06-30 04:52:44,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:52:44,591] [INFO] Task started: CheckM
[2023-06-30 04:52:44,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024103175.1_ASM2410317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024103175.1_ASM2410317v1_genomic.fna/checkm_input GCA_024103175.1_ASM2410317v1_genomic.fna/checkm_result
[2023-06-30 04:54:22,883] [INFO] Task succeeded: CheckM
[2023-06-30 04:54:22,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 04:54:22,912] [INFO] ===== Completeness check finished =====
[2023-06-30 04:54:22,913] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:54:22,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024103175.1_ASM2410317v1_genomic.fna/markers.fasta)
[2023-06-30 04:54:22,913] [INFO] Task started: Blastn
[2023-06-30 04:54:22,914] [INFO] Running command: blastn -query GCA_024103175.1_ASM2410317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98681710-e107-4d56-86b2-91085ab3bbda/dqc_reference/reference_markers_gtdb.fasta -out GCA_024103175.1_ASM2410317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:54:23,763] [INFO] Task succeeded: Blastn
[2023-06-30 04:54:23,769] [INFO] Selected 22 target genomes.
[2023-06-30 04:54:23,769] [INFO] Target genome list was writen to GCA_024103175.1_ASM2410317v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:54:23,776] [INFO] Task started: fastANI
[2023-06-30 04:54:23,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d2827d3-27f6-475d-8335-32922e7b051c/GCA_024103175.1_ASM2410317v1_genomic.fna.gz --refList GCA_024103175.1_ASM2410317v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024103175.1_ASM2410317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:54:41,233] [INFO] Task succeeded: fastANI
[2023-06-30 04:54:41,250] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 04:54:41,250] [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
GCA_009908745.1	s__Phaeodactylibacter sp009908745	76.1326	172	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Phaeodactylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490175.1	s__WFYJ01 sp015490175	76.1227	152	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__WFYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713275.1	s__JADJPL01 sp016713275	76.1207	90	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADJPL01	95.0	98.18	95.41	0.95	0.87	5	-
GCA_013360405.1	s__JABWBR01 sp013360405	76.0513	123	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759025.1	s__Phaeodactylibacter xiamenensis	76.0277	155	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Phaeodactylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703765.1	s__JADJTT01 sp016703765	76.0072	134	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADJTT01	95.0	98.25	98.24	0.94	0.92	3	-
GCA_016715405.1	s__JABWBR01 sp016715405	75.9923	115	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707205.1	s__JADJPL01 sp016707205	75.8703	80	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADJPL01	95.0	98.92	98.80	0.91	0.90	3	-
GCF_007993045.1	s__Phaeodactylibacter luteus	75.8555	123	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Phaeodactylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003045895.1	s__Lewinella sp003045895	75.8072	116	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella	95.0	99.87	99.87	0.95	0.95	2	-
GCF_004803465.1	s__Lewinella_A litorea	75.7573	86	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698985.1	s__UBA6168 sp002698985	75.7393	83	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA6168	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494245.1	s__WGBN01 sp015494245	75.7361	52	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__WGBN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234735.1	s__UBA6168 sp016234735	75.6201	86	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA6168	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970915.1	s__Solirubrum gummosum	75.4687	88	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297645.1	s__UBA6168 sp004297645	75.4103	60	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA6168	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141805.1	s__Hymenobacter daecheongensis	75.3489	56	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018967845.1	s__Hymenobacter sp018967845	75.243	55	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.02	98.98	0.94	0.93	3	-
GCA_011321935.1	s__UBA6168 sp011321935	75.0443	61	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA6168	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787415.1	s__M3007 sp016787415	74.9996	52	2221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:54:41,254] [INFO] GTDB search result was written to GCA_024103175.1_ASM2410317v1_genomic.fna/result_gtdb.tsv
[2023-06-30 04:54:41,255] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:54:41,264] [INFO] DFAST_QC result json was written to GCA_024103175.1_ASM2410317v1_genomic.fna/dqc_result.json
[2023-06-30 04:54:41,264] [INFO] DFAST_QC completed!
[2023-06-30 04:54:41,264] [INFO] Total running time: 0h2m56s