[2023-06-30 08:34:59,777] [INFO] DFAST_QC pipeline started.
[2023-06-30 08:34:59,780] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 08:34:59,780] [INFO] DQC Reference Directory: /var/lib/cwl/stg97527a78-4253-471f-a1d0-78ec568ffd08/dqc_reference
[2023-06-30 08:35:03,131] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 08:35:03,138] [INFO] Task started: Prodigal
[2023-06-30 08:35:03,139] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2aac74f-9265-4176-a5dc-54da32b93006/GCA_025345985.1_ASM2534598v1_genomic.fna.gz | prodigal -d GCA_025345985.1_ASM2534598v1_genomic.fna/cds.fna -a GCA_025345985.1_ASM2534598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 08:35:05,479] [INFO] Task succeeded: Prodigal
[2023-06-30 08:35:05,480] [INFO] Task started: HMMsearch
[2023-06-30 08:35:05,480] [INFO] Running command: hmmsearch --tblout GCA_025345985.1_ASM2534598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97527a78-4253-471f-a1d0-78ec568ffd08/dqc_reference/reference_markers.hmm GCA_025345985.1_ASM2534598v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 08:35:05,752] [INFO] Task succeeded: HMMsearch
[2023-06-30 08:35:05,755] [INFO] Found 6/6 markers.
[2023-06-30 08:35:05,788] [INFO] Query marker FASTA was written to GCA_025345985.1_ASM2534598v1_genomic.fna/markers.fasta
[2023-06-30 08:35:05,789] [INFO] Task started: Blastn
[2023-06-30 08:35:05,789] [INFO] Running command: blastn -query GCA_025345985.1_ASM2534598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97527a78-4253-471f-a1d0-78ec568ffd08/dqc_reference/reference_markers.fasta -out GCA_025345985.1_ASM2534598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:35:07,521] [INFO] Task succeeded: Blastn
[2023-06-30 08:35:07,526] [INFO] Selected 25 target genomes.
[2023-06-30 08:35:07,527] [INFO] Target genome list was writen to GCA_025345985.1_ASM2534598v1_genomic.fna/target_genomes.txt
[2023-06-30 08:35:07,553] [INFO] Task started: fastANI
[2023-06-30 08:35:07,553] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2aac74f-9265-4176-a5dc-54da32b93006/GCA_025345985.1_ASM2534598v1_genomic.fna.gz --refList GCA_025345985.1_ASM2534598v1_genomic.fna/target_genomes.txt --output GCA_025345985.1_ASM2534598v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 08:35:15,858] [INFO] Task succeeded: fastANI
[2023-06-30 08:35:15,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97527a78-4253-471f-a1d0-78ec568ffd08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 08:35:15,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97527a78-4253-471f-a1d0-78ec568ffd08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 08:35:15,873] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2023-06-30 08:35:15,873] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 08:35:15,874] [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
Lactobacillus iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	98.5866	364	421	95	conclusive
Lactobacillus iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	98.5746	361	421	95	conclusive
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	78.327	74	421	95	below_threshold
Lactobacillus hominis	strain=type strain:CRBIP 24.179	GCA_000296835.1	1203033	1203033	type	True	78.286	80	421	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	78.2472	82	421	95	below_threshold
Lactobacillus hominis	strain=DSM 23910	GCA_001436125.1	1203033	1203033	type	True	78.2	77	421	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	78.1477	88	421	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003584685.1	2107999	2107999	type	True	78.096	82	421	95	below_threshold
Lactobacillus mulieris	strain=c10Ua161M	GCA_007095465.1	2508708	2508708	type	True	77.343	63	421	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	77.2815	69	421	95	below_threshold
Lactobacillus hamsteri	strain=JCM 6256	GCA_000615445.1	96565	96565	type	True	77.154	67	421	95	below_threshold
Lactobacillus jensenii	strain=DSM 20557	GCA_001436455.1	109790	109790	type	True	77.128	66	421	95	below_threshold
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	77.1107	70	421	95	below_threshold
Lactobacillus jensenii	strain=ATCC 25258	GCA_018094625.1	109790	109790	type	True	77.0559	70	421	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 08:35:15,876] [INFO] DFAST Taxonomy check result was written to GCA_025345985.1_ASM2534598v1_genomic.fna/tc_result.tsv
[2023-06-30 08:35:15,877] [INFO] ===== Taxonomy check completed =====
[2023-06-30 08:35:15,877] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 08:35:15,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97527a78-4253-471f-a1d0-78ec568ffd08/dqc_reference/checkm_data
[2023-06-30 08:35:15,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 08:35:15,907] [INFO] Task started: CheckM
[2023-06-30 08:35:15,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025345985.1_ASM2534598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025345985.1_ASM2534598v1_genomic.fna/checkm_input GCA_025345985.1_ASM2534598v1_genomic.fna/checkm_result
[2023-06-30 08:35:31,565] [INFO] Task succeeded: CheckM
[2023-06-30 08:35:31,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 08:35:31,589] [INFO] ===== Completeness check finished =====
[2023-06-30 08:35:31,590] [INFO] ===== Start GTDB Search =====
[2023-06-30 08:35:31,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025345985.1_ASM2534598v1_genomic.fna/markers.fasta)
[2023-06-30 08:35:31,591] [INFO] Task started: Blastn
[2023-06-30 08:35:31,591] [INFO] Running command: blastn -query GCA_025345985.1_ASM2534598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97527a78-4253-471f-a1d0-78ec568ffd08/dqc_reference/reference_markers_gtdb.fasta -out GCA_025345985.1_ASM2534598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:35:32,375] [INFO] Task succeeded: Blastn
[2023-06-30 08:35:32,379] [INFO] Selected 27 target genomes.
[2023-06-30 08:35:32,380] [INFO] Target genome list was writen to GCA_025345985.1_ASM2534598v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 08:35:32,410] [INFO] Task started: fastANI
[2023-06-30 08:35:32,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2aac74f-9265-4176-a5dc-54da32b93006/GCA_025345985.1_ASM2534598v1_genomic.fna.gz --refList GCA_025345985.1_ASM2534598v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025345985.1_ASM2534598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 08:35:40,477] [INFO] Task succeeded: fastANI
[2023-06-30 08:35:40,492] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 08:35:40,492] [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_000160875.1	s__Lactobacillus iners	98.5866	364	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	conclusive
GCF_000014425.1	s__Lactobacillus gasseri	78.327	74	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	-
GCF_000296835.1	s__Lactobacillus hominis	78.286	80	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
GCF_003423665.1	s__Lactobacillus rodentium	78.2108	86	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584685.1	s__Lactobacillus paragasseri	78.096	82	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCF_017874575.1	s__Lactobacillus colini	77.7889	75	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589675.1	s__Lactobacillus sp910589675	77.7792	79	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCF_007095465.1	s__Lactobacillus mulieris	77.343	63	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.54	96.91	0.92	0.85	18	-
GCF_001434975.1	s__Lactobacillus gallinarum	77.2815	69	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCA_018883635.1	s__Lactobacillus pullistercoris	77.2222	52	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000615445.1	s__Lactobacillus hamsteri	77.154	67	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001436455.1	s__Lactobacillus jensenii	77.128	66	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.86	99.75	0.93	0.88	31	-
GCF_014323605.1	s__Lactobacillus kimbladii_B	76.9503	51	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570935.1	s__Lactobacillus sp007570935	76.9451	67	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004009905.1	s__Lactobacillus xujianguonis	76.877	56	421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-30 08:35:40,496] [INFO] GTDB search result was written to GCA_025345985.1_ASM2534598v1_genomic.fna/result_gtdb.tsv
[2023-06-30 08:35:40,497] [INFO] ===== GTDB Search completed =====
[2023-06-30 08:35:40,502] [INFO] DFAST_QC result json was written to GCA_025345985.1_ASM2534598v1_genomic.fna/dqc_result.json
[2023-06-30 08:35:40,502] [INFO] DFAST_QC completed!
[2023-06-30 08:35:40,503] [INFO] Total running time: 0h0m41s