[2024-01-24 14:19:02,502] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:02,504] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:02,504] [INFO] DQC Reference Directory: /var/lib/cwl/stge865640a-50e0-4d98-a837-af2b593118db/dqc_reference
[2024-01-24 14:19:03,726] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:03,727] [INFO] Task started: Prodigal
[2024-01-24 14:19:03,727] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd0e0cef-1fbc-4d48-b239-afe6979be5e1/GCF_019050325.1_ASM1905032v1_genomic.fna.gz | prodigal -d GCF_019050325.1_ASM1905032v1_genomic.fna/cds.fna -a GCF_019050325.1_ASM1905032v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:21,965] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:21,965] [INFO] Task started: HMMsearch
[2024-01-24 14:19:21,965] [INFO] Running command: hmmsearch --tblout GCF_019050325.1_ASM1905032v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge865640a-50e0-4d98-a837-af2b593118db/dqc_reference/reference_markers.hmm GCF_019050325.1_ASM1905032v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:22,327] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:22,328] [INFO] Found 6/6 markers.
[2024-01-24 14:19:22,384] [INFO] Query marker FASTA was written to GCF_019050325.1_ASM1905032v1_genomic.fna/markers.fasta
[2024-01-24 14:19:22,384] [INFO] Task started: Blastn
[2024-01-24 14:19:22,384] [INFO] Running command: blastn -query GCF_019050325.1_ASM1905032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge865640a-50e0-4d98-a837-af2b593118db/dqc_reference/reference_markers.fasta -out GCF_019050325.1_ASM1905032v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:23,617] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:23,620] [INFO] Selected 24 target genomes.
[2024-01-24 14:19:23,621] [INFO] Target genome list was writen to GCF_019050325.1_ASM1905032v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:23,630] [INFO] Task started: fastANI
[2024-01-24 14:19:23,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd0e0cef-1fbc-4d48-b239-afe6979be5e1/GCF_019050325.1_ASM1905032v1_genomic.fna.gz --refList GCF_019050325.1_ASM1905032v1_genomic.fna/target_genomes.txt --output GCF_019050325.1_ASM1905032v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:57,869] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:57,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge865640a-50e0-4d98-a837-af2b593118db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:57,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge865640a-50e0-4d98-a837-af2b593118db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:57,889] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:57,889] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:57,889] [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
[Mycobacterium] fortunisiensis	strain=TNTM28	GCA_019050325.1	2600579	2600579	type	True	100.0	1811	1815	95	conclusive
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	85.8563	1447	1815	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	85.8349	1433	1815	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	85.8324	1449	1815	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	85.79	1448	1815	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	85.7442	1440	1815	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	85.3183	1383	1815	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	85.1891	1347	1815	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	85.1341	1409	1815	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	85.0833	1401	1815	95	below_threshold
Mycolicibacterium setense	strain=DSM 45070	GCA_000805385.1	431269	431269	type	True	85.052	1421	1815	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	85.0104	1443	1815	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	82.2446	1206	1815	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	82.2228	1204	1815	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	81.9583	1158	1815	95	below_threshold
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	81.8336	1122	1815	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.6255	784	1815	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	80.6159	776	1815	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	80.2018	863	1815	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	80.0569	872	1815	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.955	798	1815	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.778	837	1815	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	79.6811	850	1815	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5734	845	1815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:57,891] [INFO] DFAST Taxonomy check result was written to GCF_019050325.1_ASM1905032v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:57,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:57,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:57,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge865640a-50e0-4d98-a837-af2b593118db/dqc_reference/checkm_data
[2024-01-24 14:19:57,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:57,946] [INFO] Task started: CheckM
[2024-01-24 14:19:57,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019050325.1_ASM1905032v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019050325.1_ASM1905032v1_genomic.fna/checkm_input GCF_019050325.1_ASM1905032v1_genomic.fna/checkm_result
[2024-01-24 14:21:06,356] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:06,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:06,379] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:06,380] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:06,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019050325.1_ASM1905032v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:06,380] [INFO] Task started: Blastn
[2024-01-24 14:21:06,381] [INFO] Running command: blastn -query GCF_019050325.1_ASM1905032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge865640a-50e0-4d98-a837-af2b593118db/dqc_reference/reference_markers_gtdb.fasta -out GCF_019050325.1_ASM1905032v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:07,991] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:07,994] [INFO] Selected 17 target genomes.
[2024-01-24 14:21:07,995] [INFO] Target genome list was writen to GCF_019050325.1_ASM1905032v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:08,007] [INFO] Task started: fastANI
[2024-01-24 14:21:08,007] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd0e0cef-1fbc-4d48-b239-afe6979be5e1/GCF_019050325.1_ASM1905032v1_genomic.fna.gz --refList GCF_019050325.1_ASM1905032v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019050325.1_ASM1905032v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:31,860] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:31,879] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:31,880] [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_019050325.1	s__Mycobacterium fortunisiensis	100.0	1811	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000455325.1	s__Mycobacterium septicum	85.8517	1446	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_009729095.1	s__Mycobacterium sp009729095	85.8316	1378	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.96	1.00	1.00	6	-
GCF_010731295.1	s__Mycobacterium boenickei	85.7777	1449	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_001942045.1	s__Mycobacterium porcinum_A	85.5916	1378	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086835.1	s__Mycobacterium porcinum	85.4012	1416	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_001954135.1	s__Mycobacterium sp001954135	85.3424	1345	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078665.2	s__Mycobacterium houstonense	85.3352	1381	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942625.1	s__Mycobacterium syngnathidarum	85.1042	1417	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
GCF_000295855.1	s__Mycobacterium fortuitum	85.0629	1406	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_000805385.1	s__Mycobacterium setense	85.0549	1420	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	98.47	0.95	0.89	4	-
GCF_002157835.1	s__Mycobacterium dioxanotrophicus	81.9863	1155	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665685.1	s__Mycobacterium sp001665685	81.7156	1108	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	80.7477	971	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570485.1	s__Mycobacterium novocastrense	79.8753	873	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCA_900637135.1	s__Mycobacterium flavescens	79.7739	844	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_000230935.1	s__Mycobacterium rhodesiae_B	79.5418	856	1815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:31,882] [INFO] GTDB search result was written to GCF_019050325.1_ASM1905032v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:31,882] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:31,886] [INFO] DFAST_QC result json was written to GCF_019050325.1_ASM1905032v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:31,887] [INFO] DFAST_QC completed!
[2024-01-24 14:21:31,887] [INFO] Total running time: 0h2m29s