[2023-06-08 07:43:03,264] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:43:03,267] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:43:03,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg9abeb5b5-00cc-4d94-a6a1-81a4541b82ca/dqc_reference
[2023-06-08 07:43:05,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:43:05,648] [INFO] Task started: Prodigal
[2023-06-08 07:43:05,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg62baca3f-9d63-4731-b4d0-7060f1dcb0ac/GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:43:09,130] [INFO] Task succeeded: Prodigal
[2023-06-08 07:43:09,131] [INFO] Task started: HMMsearch
[2023-06-08 07:43:09,131] [INFO] Running command: hmmsearch --tblout GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9abeb5b5-00cc-4d94-a6a1-81a4541b82ca/dqc_reference/reference_markers.hmm GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:43:09,362] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:43:09,364] [INFO] Found 6/6 markers.
[2023-06-08 07:43:09,387] [INFO] Query marker FASTA was written to GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 07:43:09,387] [INFO] Task started: Blastn
[2023-06-08 07:43:09,387] [INFO] Running command: blastn -query GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9abeb5b5-00cc-4d94-a6a1-81a4541b82ca/dqc_reference/reference_markers.fasta -out GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:43:09,972] [INFO] Task succeeded: Blastn
[2023-06-08 07:43:09,998] [INFO] Selected 21 target genomes.
[2023-06-08 07:43:09,999] [INFO] Target genome list was writen to GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 07:43:10,006] [INFO] Task started: fastANI
[2023-06-08 07:43:10,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg62baca3f-9d63-4731-b4d0-7060f1dcb0ac/GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:43:16,711] [INFO] Task succeeded: fastANI
[2023-06-08 07:43:16,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9abeb5b5-00cc-4d94-a6a1-81a4541b82ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:43:16,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9abeb5b5-00cc-4d94-a6a1-81a4541b82ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:43:16,728] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:43:16,728] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 07:43:16,729] [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 hominis	strain=type strain:CRBIP 24.179	GCA_000296835.1	1203033	1203033	type	True	83.0588	396	611	95	below_threshold
Lactobacillus hominis	strain=DSM 23910	GCA_001436125.1	1203033	1203033	type	True	82.9866	400	611	95	below_threshold
Lactobacillus johnsonii	strain=ATCC 33200	GCA_000159355.1	33959	33959	type	True	80.1106	218	611	95	below_threshold
Lactobacillus taiwanensis	strain=DSM 21401	GCA_001436695.1	508451	508451	type	True	80.0756	209	611	95	below_threshold
Lactobacillus johnsonii	strain=ATCC 33200	GCA_001433975.1	33959	33959	type	True	80.0077	217	611	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	79.88	215	611	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003584685.1	2107999	2107999	type	True	79.7979	222	611	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_008868295.1	1596	1596	type	True	79.5723	208	611	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	79.513	220	611	95	below_threshold
Lactobacillus gasseri	strain=NCTC13722	GCA_900452355.1	1596	1596	type	True	79.4985	215	611	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	79.1905	172	611	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_001435325.1	151781	151781	type	True	79.1873	147	611	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_003423665.1	947835	947835	type	True	79.1786	175	611	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	79.1367	149	611	95	below_threshold
Lactobacillus colini	strain=DSM 101872	GCA_017874575.1	1819254	1819254	type	True	78.9137	174	611	95	below_threshold
Lactobacillus iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	77.8447	80	611	95	below_threshold
Lactobacillus iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	77.8408	84	611	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:43:16,731] [INFO] DFAST Taxonomy check result was written to GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 07:43:16,731] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:43:16,731] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:43:16,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9abeb5b5-00cc-4d94-a6a1-81a4541b82ca/dqc_reference/checkm_data
[2023-06-08 07:43:16,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:43:16,759] [INFO] Task started: CheckM
[2023-06-08 07:43:16,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 07:43:34,907] [INFO] Task succeeded: CheckM
[2023-06-08 07:43:34,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:43:34,930] [INFO] ===== Completeness check finished =====
[2023-06-08 07:43:34,930] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:43:34,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 07:43:34,931] [INFO] Task started: Blastn
[2023-06-08 07:43:34,931] [INFO] Running command: blastn -query GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9abeb5b5-00cc-4d94-a6a1-81a4541b82ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:43:35,667] [INFO] Task succeeded: Blastn
[2023-06-08 07:43:35,671] [INFO] Selected 19 target genomes.
[2023-06-08 07:43:35,671] [INFO] Target genome list was writen to GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:43:35,695] [INFO] Task started: fastANI
[2023-06-08 07:43:35,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg62baca3f-9d63-4731-b4d0-7060f1dcb0ac/GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:43:41,928] [INFO] Task succeeded: fastANI
[2023-06-08 07:43:41,949] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 07:43:41,949] [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_000296835.1	s__Lactobacillus hominis	83.0588	396	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
GCF_000159355.1	s__Lactobacillus johnsonii	80.0844	219	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.89	95.28	0.86	0.57	61	-
GCF_001436695.1	s__Lactobacillus taiwanensis	80.0756	209	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.80	98.01	0.90	0.86	31	-
GCA_910589675.1	s__Lactobacillus sp910589675	80.0618	171	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCA_910589175.1	s__Lactobacillus sp910589175	79.8385	232	611	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	79.7979	222	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCA_014803905.1	s__Lactobacillus sp014803905	79.5596	118	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014425.1	s__Lactobacillus gasseri	79.513	220	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	-
GCA_014803895.1	s__Lactobacillus sp014803895	79.4297	174	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435325.1	s__Lactobacillus intestinalis	79.1589	147	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	-
GCF_003423665.1	s__Lactobacillus rodentium	79.1526	176	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874575.1	s__Lactobacillus colini	78.9137	174	611	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	78.7002	139	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000615285.1	s__Lactobacillus kitasatonis	78.5725	131	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCA_018883635.1	s__Lactobacillus pullistercoris	77.9818	135	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000160875.1	s__Lactobacillus iners	77.8544	83	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	-
GCF_016100975.1	s__Lactobacillus sp016100975	77.6789	58	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014323605.1	s__Lactobacillus kimbladii_B	77.2699	63	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970755.1	s__Lactobacillus kimbladii_A	77.0952	66	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 07:43:41,951] [INFO] GTDB search result was written to GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 07:43:41,952] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:43:41,956] [INFO] DFAST_QC result json was written to GCA_947367085.1_SRR15429248_bin.2_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 07:43:41,956] [INFO] DFAST_QC completed!
[2023-06-08 07:43:41,957] [INFO] Total running time: 0h0m39s